This is an R Markdown Notebook. When you execute code within the notebook, the results appear beneath the code.

Try executing this chunk by clicking the Run button within the chunk or by placing your cursor inside it and pressing Cmd+Shift+Enter.

library("devtools")
install_github("jw156605/SLICER")
Skipping install of 'SLICER' from a github remote, the SHA1 (cb1be8ac) has not changed since last install.
  Use `force = TRUE` to force installation
library(Seurat)
library(readr)
library(tidyverse)
library(HGC) 
library(latticeExtra)
library(lattice) 
library(RColorBrewer)
library(clusterProfiler)
library(org.Mm.eg.db)
library(AnnotationDbi)
exp = read_csv("normalized_data.csv")
New names:
• `` -> `...1`
• `` -> `...151`
• `` -> `...240`
• `` -> `...289`
• `` -> `...352`
• `` -> `...391`
• `` -> `...394`
• `` -> `...450`
• `` -> `...462`
Rows: 14414 Columns: 463
── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────
Delimiter: ","
chr   (1): ...1
dbl (454): M1_A01, M1_A02, M1_A03, M1_A05, M1_A06, M1_A08, M1_A09, M1_A10, M1_B01, M1_B03, M1_B04, M1_B05, M1_B06, M...
lgl   (8): ...151, ...240, ...289, ...352, ...391, ...394, ...450, ...462

ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
exp = discard(exp,~all(is.na(.) |.  == ""))
exp = distinct(exp, `...1`, .keep_all = TRUE)
# filtering out the reprogramming transcription factors 
exp = filter(exp, !`...1`%in% c("Mef2c", "Gata4", "Tbx5"))
exp = column_to_rownames(exp, var="...1")

seurat.obj = CreateSeuratObject(counts = exp)
seurat.obj = NormalizeData(seurat.obj)
Performing log-normalization
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
seurat.obj = FindVariableFeatures(seurat.obj, selection.method =  "vst", nfeatures = 10000)
Calculating gene variances
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
all.genes = rownames(seurat.obj)
seurat.obj = ScaleData(seurat.obj, features = all.genes)
Centering and scaling data matrix

  |                                                                                                                    
  |                                                                                                              |   0%
  |                                                                                                                    
  |=======                                                                                                       |   7%
  |                                                                                                                    
  |===============                                                                                               |  13%
  |                                                                                                                    
  |======================                                                                                        |  20%
  |                                                                                                                    
  |=============================                                                                                 |  27%
  |                                                                                                                    
  |=====================================                                                                         |  33%
  |                                                                                                                    
  |============================================                                                                  |  40%
  |                                                                                                                    
  |===================================================                                                           |  47%
  |                                                                                                                    
  |===========================================================                                                   |  53%
  |                                                                                                                    
  |==================================================================                                            |  60%
  |                                                                                                                    
  |=========================================================================                                     |  67%
  |                                                                                                                    
  |=================================================================================                             |  73%
  |                                                                                                                    
  |========================================================================================                      |  80%
  |                                                                                                                    
  |===============================================================================================               |  87%
  |                                                                                                                    
  |=======================================================================================================       |  93%
  |                                                                                                                    
  |==============================================================================================================| 100%
seurat.obj = RunPCA(seurat.obj, features =  VariableFeatures(seurat.obj))
PC_ 1 
Positive:  Ehd4, Acaa2, Dsp, Ldhb, Nid2, Ryr2, Myl4, Epb4.1, Smpx, Tnni3 
       Ttn, Tnnt2, Mgst3, Sort1, Ldb3, Jup, Mlf1, Baiap2l1, Rrad, Mgrn1 
       Fryl, Ppp1r3c, Fam134b, Fabp3, Cenpa, Usp28, Clu, Pcyt1a, Ddit4l, Cd24a 
Negative:  Fstl1, Bgn, Cd200, Col3a1, Rbp1, Tagln2, Fam198b, Postn, Col1a2, Tagln 
       Fbln2, Rbms3, Lox, Fbn1, Loxl1, Dhrs3, Marcks, Col8a1, 11-Sep, Col5a2 
       Clca1, Lrrc8a, Spry2, Anxa1, Ogn, Nars, Gstm2, Fbln5, Asns, Acta2 
PC_ 2 
Positive:  Top2a, Prc1, Smc2, Ccnb1, Birc5, Cdk1, Ube2c, Rrm2, Mki67, Pbk 
       Ckap2l, Asf1b, Cks2, Tpx2, Cdca8, Kif20b, 2810417H13Rik, Cks1b, Anln, Tacc3 
       Spc25, Hmmr, Hmgb2, Shcbp1, Ndc80, Mad2l1, Nuf2, Cenpe, Ect2, Cdca2 
Negative:  Cst3, B2m, Sptbn1, Malat1, Ypel5, Itm2b, Gyg, Parp3, Tspyl1, Serpine2 
       Lama2, Igfbp7, Ogn, B4galt1, Gpx3, Ctsa, Asah1, Pdcd4, Itgb5, Fhl2 
       Pam, Col4a2, Lhfp, Tcn2, Mxra8, Smim14, Ctsd, Akap13, Prex2, Impact 
PC_ 3 
Positive:  Cst3, Col4a1, Flna, Igfbp7, Col1a1, Col4a2, Myl9, Sorbs2, Fhl2, Itgb1 
       Tns1, Col14a1, Ankrd1, Tpm2, Lbh, Pcolce, Tuba1a, Postn, Tuba1b, Itga1 
       Col5a1, Actn4, Pdlim2, Myom1, Pdgfrb, Tbx20, Sorbs1, Acta2, Pcdh18, Macf1 
Negative:  Gpm6a, Mgst1, Hpgd, Gsta4, Ptgs1, Upk1b, Pkhd1l1, F11r, Msln, Bst1 
       Maf, Ezr, Mpzl2, Cxadr, Krt8, Cd55, Igfbp6, Igfbp4, Acsl4, Bex4 
       Gcnt1, Vnn1, Ftl1, Efna5, Slpi, Ptp4a2, Tmem108, Tmem154, Csde1, Bnc1 
PC_ 4 
Positive:  S100a6, Tpm1, Tpm4, Actb, Nme1, Zyx, Lgals1, Tpm2, Cryab, Actg1 
       Wisp1, Gapdh, Gm12070, Actn1, Timp1, Slc25a5, Sec13, Eif5a, Psat1, Creb3l1 
       Tnfrsf12a, Ccnd2, Csf1, Pkm, Pcolce, Acta2, Des, Rcn3, Col1a1, Wdr1 
Negative:  Egfl7, Ctla2a, Gja4, Emcn, Cdh5, Notch1, Klhl4, Gimap6, Pecam1, Stab1 
       Gpr116, Lyl1, Tie1, Entpd1, Ctla2b, Fli1, Myct1, Sox7, Thsd1, Eltd1 
       Gngt2, Mmrn2, S1pr1, Mecom, Tgfbi, Klhl24, Tmem2, Apoe, Plxnd1, Akap13 
PC_ 5 
Positive:  Egfl7, Notch1, Klhl4, Stab1, Cdh5, Emcn, Cgnl1, Pecam1, Gja4, Ramp2 
       Lyl1, Col4a1, Gpr116, Tie1, Entpd1, Zfp69, Loxl2, Eltd1, Plxnd1, Thsd1 
       Cxcl16, Col5a1, Tek, S1pr1, Txndc5, Tgfbi, Odc1, Eng, Sox7, Myct1 
Negative:  Spcs3, Impact, Ypel5, Cpne8, Lnp, Arhgap44, Sptbn1, Myo10, Nexn, Arid5b 
       Arl5a, Braf, Klhl9, Cpne3, Lama2, Mrfap1, Serping1, Mlf1, Zdhhc2, Mier3 
       Gm2a, Dstn, Emc2, Myoz2, Ncam1, Rhobtb3, Cryab, Gucy1a3, Ttn, Idh1 
ElbowPlot(seurat.obj)
seurat.obj = FindNeighbors(seurat.obj, dims = 1:15)
Computing nearest neighbor graph
Computing SNN
seurat.obj = FindClusters(seurat.obj, resolution = 1.75)
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 454
Number of edges: 16805

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.4797
Number of communities: 8
Elapsed time: 0 seconds
identified_cells = read.csv("paper_cell_states.csv", row.names = 1, header=TRUE)
identified_cells = identified_cells[match(rownames(seurat.obj@meta.data), rownames(identified_cells)),]
seurat.obj@meta.data$cc_paper = identified_cells$CC
seurat.obj@meta.data$cat_paper = identified_cells$stage
seurat.obj@meta.data$cc_hclust = "CCI"
seurat.obj@meta.data[active_cells,]$cc_hclust = "CCA"
Idents(seurat.obj)  = "RNA_snn_res.1.75"
seurat.obj = RunUMAP(seurat.obj, dims = 1:15)
Warning: The default method for RunUMAP has changed from calling Python UMAP via reticulate to the R-native UWOT using the cosine metric
To use Python UMAP via reticulate, set umap.method to 'umap-learn' and metric to 'correlation'
This message will be shown once per session
17:59:25 UMAP embedding parameters a = 0.9922 b = 1.112
17:59:25 Read 454 rows and found 15 numeric columns
17:59:25 Using Annoy for neighbor search, n_neighbors = 30
17:59:25 Building Annoy index with metric = cosine, n_trees = 50
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
17:59:25 Writing NN index file to temp file /var/folders/fj/09brpj8s5mz1c5wxktl80s080000gn/T//RtmpE0XJwn/file8ed51e4226b8
17:59:25 Searching Annoy index using 1 thread, search_k = 3000
17:59:25 Annoy recall = 100%
17:59:26 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
17:59:27 Initializing from normalized Laplacian + noise (using irlba)
17:59:27 Commencing optimization for 500 epochs, with 17028 positive edges
Using method 'umap'
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
17:59:28 Optimization finished
clusters = DimPlot(seurat.obj, group.by = "RNA_snn_res.1.75", label = TRUE, reduction = "umap")
condition = DimPlot(seurat.obj, group.by = "cc_paper", label = TRUE, reduction = "umap")

condition|clusters

seurat.obj = RunTSNE(seurat.obj, dims = 1:15)
DimPlot(seurat.obj, reduction = "tsne", group.by = 'RNA_snn_res.1.75')

markers = FindAllMarkers(seurat.obj, logfc.threshold =  0.25, min.pct = 0.1, only.pos = FALSE, test.use = 'MAST')
top_markers = markers %>%
    group_by(cluster) %>%
    slice_max(n = 2, order_by = avg_log2FC)
FeaturePlot(seurat.obj, features = c("Dhrs3"), min.cutoff = 'q10')

VlnPlot(seurat.obj, features = c("Rbp1", "Dhrs3"))

VlnPlot(seurat.obj, features = c("Fstl1", "Bgn"))

VlnPlot(seurat.obj, features = c("Serpinh1", "Dsp"))

VlnPlot(seurat.obj, features = c("Prc1", "Birc5"))

## cell cycle 
s.genes <- str_to_title(cc.genes$s.genes)
g2m.genes <- str_to_title(cc.genes$g2m.genes)

seurat.obj = CellCycleScoring(seurat.obj, s.features = s.genes, g2m.features = g2m.genes)
clusters = DimPlot(seurat.obj, group.by = "RNA_snn_res.1.75", label = TRUE, reduction = "umap")
real_condition = DimPlot(seurat.obj, group.by = "cc_paper", label = TRUE, reduction = "umap") 
phase = DimPlot(seurat.obj, group.by = "Phase", label = TRUE, reduction = "umap") 
cat = DimPlot(seurat.obj, group.by = "cc_hclust", label = TRUE, reduction = "umap") 

clusters|real_condition|phase|cat

NA
NA

subsetting the cells that fit with hclust and performing clustering on each group

subset(x = seurat.obj, subset = cc_hclust == "CCA")
An object of class Seurat 
14410 features across 80 samples within 1 assay 
Active assay: RNA (14410 features, 10000 variable features)
 3 dimensional reductions calculated: pca, umap, tsne

clustering CCI cels

cci_seurat = FindNeighbors(cci_seurat, dims = 1:15)
cci_seurat = FindClusters(cci_seurat, resolution = 1)
cl= DimPlot(cci_seurat, group.by = "RNA_snn_res.1",label = TRUE)
pap = DimPlot(cci_seurat, group.by = "cat_paper", label = TRUE)
cl|pap

identifying CCI cells

cci_markers = FindAllMarkers(cci_seurat, logfc.threshold =  0.25, min.pct = 0.1, only.pos = FALSE, test.use = 'MAST')
cci_top_markers = cci_markers %>%
    group_by(cluster) %>%
    slice_min(n = 5, order_by = p_val_adj)
VlnPlot(cci_seurat, features = c("Fstl1", "Bgn"))

VlnPlot(cci_seurat, features = c("Tnni3", "Smpx"))

VlnPlot(cci_seurat, features = c("Serpinh1", "Dsp"))

VlnPlot(cci_seurat, features = c("Clca2", "Rbp1"))

VlnPlot(cci_seurat, features = c("Cfh", "B4galt1"))

Fstl1 involved in endothelial cell differentiation and endothelial cell migration and Bgn is a gene that is used for connective tissue metabolism -> lower expression -> cluster 0 = iCM

Tnni3, smpx, dsp used for cardiomycoytes -> cluster 2 = pre-iCM, cluster 1 and 3 are still fibroblasts

cluseter 1 further away from cluster 0 = fibroblastr clusetr 3 = induced fibroblasts

Idents(cci_seurat)  = "RNA_snn_res.1"
cci_seurat = RenameIdents(cci_seurat, `0` = "iCM")
cci_seurat = RenameIdents(cci_seurat, `1` = "Fib")
cci_seurat = RenameIdents(cci_seurat, `2` = "piCM")
cci_seurat = RenameIdents(cci_seurat, `3` = "iFib")

clustering CCA cells

cca_seurat = FindClusters(cca_seurat, resolution = 1)
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 80
Number of edges: 2244

Running Louvain algorithm...
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.2948
Number of communities: 3
Elapsed time: 0 seconds
cl= DimPlot(cca_seurat, group.by = "RNA_snn_res.1",label = TRUE)

pap = DimPlot(cca_seurat, group.by = "cat_paper", label = TRUE)
cl|pap

identifying CCA cells

cca_markers = FindAllMarkers(cca_seurat, logfc.threshold =  0.25, min.pct = 0.1, only.pos = FALSE, test.use = 'MAST')
Calculating cluster 0

 Completed [=====>-------------------------------------------------------------------------------------------------]   6% with 0 failures
 Completed [======>------------------------------------------------------------------------------------------------]   6% with 0 failures
 Completed [======>------------------------------------------------------------------------------------------------]   7% with 0 failures
 Completed [=======>-----------------------------------------------------------------------------------------------]   7% with 0 failures
 Completed [=======>-----------------------------------------------------------------------------------------------]   8% with 0 failures
 Completed [========>----------------------------------------------------------------------------------------------]   8% with 0 failures
 Completed [========>----------------------------------------------------------------------------------------------]   9% with 0 failures
 Completed [=========>---------------------------------------------------------------------------------------------]   9% with 0 failures
 Completed [=========>---------------------------------------------------------------------------------------------]  10% with 0 failures
 Completed [==========>--------------------------------------------------------------------------------------------]  10% with 0 failures
 Completed [==========>--------------------------------------------------------------------------------------------]  11% with 0 failures
 Completed [===========>-------------------------------------------------------------------------------------------]  11% with 0 failures
 Completed [===========>-------------------------------------------------------------------------------------------]  12% with 0 failures
 Completed [============>------------------------------------------------------------------------------------------]  12% with 0 failures
 Completed [============>------------------------------------------------------------------------------------------]  13% with 0 failures
 Completed [=============>-----------------------------------------------------------------------------------------]  13% with 0 failures
 Completed [=============>-----------------------------------------------------------------------------------------]  14% with 0 failures
 Completed [==============>----------------------------------------------------------------------------------------]  14% with 0 failures
 Completed [==============>----------------------------------------------------------------------------------------]  15% with 0 failures
 Completed [===============>---------------------------------------------------------------------------------------]  15% with 0 failures
 Completed [===============>---------------------------------------------------------------------------------------]  16% with 0 failures
 Completed [================>--------------------------------------------------------------------------------------]  16% with 0 failures
 Completed [================>--------------------------------------------------------------------------------------]  17% with 0 failures
 Completed [=================>-------------------------------------------------------------------------------------]  17% with 0 failures
 Completed [=================>-------------------------------------------------------------------------------------]  18% with 0 failures
 Completed [==================>------------------------------------------------------------------------------------]  18% with 0 failures
 Completed [==================>------------------------------------------------------------------------------------]  19% with 0 failures
 Completed [===================>-----------------------------------------------------------------------------------]  19% with 0 failures
 Completed [===================>-----------------------------------------------------------------------------------]  20% with 0 failures
 Completed [====================>----------------------------------------------------------------------------------]  20% with 0 failures
 Completed [====================>----------------------------------------------------------------------------------]  21% with 0 failures
 Completed [=====================>---------------------------------------------------------------------------------]  21% with 0 failures
 Completed [=====================>---------------------------------------------------------------------------------]  22% with 0 failures
 Completed [======================>--------------------------------------------------------------------------------]  22% with 0 failures
 Completed [======================>--------------------------------------------------------------------------------]  23% with 0 failures
 Completed [=======================>-------------------------------------------------------------------------------]  23% with 0 failures
 Completed [=======================>-------------------------------------------------------------------------------]  24% with 0 failures
 Completed [========================>------------------------------------------------------------------------------]  24% with 0 failures
 Completed [========================>------------------------------------------------------------------------------]  25% with 0 failures
 Completed [=========================>-----------------------------------------------------------------------------]  25% with 0 failures
 Completed [=========================>-----------------------------------------------------------------------------]  26% with 0 failures
 Completed [==========================>----------------------------------------------------------------------------]  26% with 0 failures
 Completed [==========================>----------------------------------------------------------------------------]  27% with 0 failures
 Completed [===========================>---------------------------------------------------------------------------]  27% with 0 failures
 Completed [===========================>---------------------------------------------------------------------------]  28% with 0 failures
 Completed [============================>--------------------------------------------------------------------------]  28% with 0 failures
 Completed [============================>--------------------------------------------------------------------------]  29% with 0 failures
 Completed [=============================>-------------------------------------------------------------------------]  29% with 0 failures
 Completed [=============================>-------------------------------------------------------------------------]  30% with 0 failures
 Completed [==============================>------------------------------------------------------------------------]  30% with 0 failures
 Completed [==============================>------------------------------------------------------------------------]  31% with 0 failures
 Completed [===============================>-----------------------------------------------------------------------]  31% with 0 failures
 Completed [===============================>-----------------------------------------------------------------------]  32% with 0 failures
 Completed [================================>----------------------------------------------------------------------]  32% with 0 failures
 Completed [================================>----------------------------------------------------------------------]  33% with 0 failures
 Completed [=================================>---------------------------------------------------------------------]  33% with 0 failures
 Completed [==================================>--------------------------------------------------------------------]  34% with 0 failures
 Completed [===================================>-------------------------------------------------------------------]  35% with 0 failures
 Completed [====================================>------------------------------------------------------------------]  35% with 0 failures
 Completed [====================================>------------------------------------------------------------------]  36% with 0 failures
 Completed [=====================================>-----------------------------------------------------------------]  36% with 0 failures
 Completed [=====================================>-----------------------------------------------------------------]  37% with 0 failures
 Completed [======================================>----------------------------------------------------------------]  37% with 0 failures
 Completed [======================================>----------------------------------------------------------------]  38% with 0 failures
 Completed [=======================================>---------------------------------------------------------------]  38% with 0 failures
 Completed [=======================================>---------------------------------------------------------------]  39% with 0 failures
 Completed [========================================>--------------------------------------------------------------]  39% with 0 failures
 Completed [========================================>--------------------------------------------------------------]  40% with 0 failures
 Completed [=========================================>-------------------------------------------------------------]  40% with 0 failures
 Completed [=========================================>-------------------------------------------------------------]  41% with 0 failures
 Completed [==========================================>------------------------------------------------------------]  41% with 0 failures
 Completed [==========================================>------------------------------------------------------------]  42% with 0 failures
 Completed [===========================================>-----------------------------------------------------------]  42% with 0 failures
 Completed [===========================================>-----------------------------------------------------------]  43% with 0 failures
 Completed [============================================>----------------------------------------------------------]  43% with 0 failures
 Completed [============================================>----------------------------------------------------------]  44% with 0 failures
 Completed [=============================================>---------------------------------------------------------]  44% with 0 failures
 Completed [=============================================>---------------------------------------------------------]  45% with 0 failures
 Completed [==============================================>--------------------------------------------------------]  45% with 0 failures
 Completed [==============================================>--------------------------------------------------------]  46% with 0 failures
 Completed [===============================================>-------------------------------------------------------]  46% with 0 failures
 Completed [===============================================>-------------------------------------------------------]  47% with 0 failures
 Completed [================================================>------------------------------------------------------]  47% with 0 failures
 Completed [================================================>------------------------------------------------------]  48% with 0 failures
 Completed [=================================================>-----------------------------------------------------]  48% with 0 failures
 Completed [=================================================>-----------------------------------------------------]  49% with 0 failures
 Completed [==================================================>----------------------------------------------------]  49% with 0 failures
 Completed [==================================================>----------------------------------------------------]  50% with 0 failures
 Completed [===================================================>---------------------------------------------------]  50% with 0 failures
 Completed [===================================================>---------------------------------------------------]  51% with 0 failures
 Completed [====================================================>--------------------------------------------------]  51% with 0 failures
 Completed [====================================================>--------------------------------------------------]  52% with 0 failures
 Completed [=====================================================>-------------------------------------------------]  52% with 0 failures
 Completed [=====================================================>-------------------------------------------------]  53% with 0 failures
 Completed [======================================================>------------------------------------------------]  53% with 0 failures
 Completed [======================================================>------------------------------------------------]  54% with 0 failures
 Completed [=======================================================>-----------------------------------------------]  54% with 0 failures
 Completed [=======================================================>-----------------------------------------------]  55% with 0 failures
 Completed [========================================================>----------------------------------------------]  55% with 0 failures
 Completed [========================================================>----------------------------------------------]  56% with 0 failures
 Completed [=========================================================>---------------------------------------------]  56% with 0 failures
 Completed [=========================================================>---------------------------------------------]  57% with 0 failures
 Completed [==========================================================>--------------------------------------------]  57% with 0 failures
 Completed [==========================================================>--------------------------------------------]  58% with 0 failures
 Completed [===========================================================>-------------------------------------------]  58% with 0 failures
 Completed [===========================================================>-------------------------------------------]  59% with 0 failures
 Completed [============================================================>------------------------------------------]  59% with 0 failures
 Completed [============================================================>------------------------------------------]  60% with 0 failures
 Completed [=============================================================>-----------------------------------------]  60% with 0 failures
 Completed [=============================================================>-----------------------------------------]  61% with 0 failures
 Completed [==============================================================>----------------------------------------]  61% with 0 failures
 Completed [==============================================================>----------------------------------------]  62% with 0 failures
 Completed [===============================================================>---------------------------------------]  62% with 0 failures
 Completed [===============================================================>---------------------------------------]  63% with 0 failures
 Completed [================================================================>--------------------------------------]  63% with 0 failures
 Completed [================================================================>--------------------------------------]  64% with 0 failures
 Completed [=================================================================>-------------------------------------]  64% with 0 failures
 Completed [=================================================================>-------------------------------------]  65% with 0 failures
 Completed [==================================================================>------------------------------------]  65% with 0 failures
 Completed [===================================================================>-----------------------------------]  66% with 0 failures
 Completed [====================================================================>----------------------------------]  67% with 0 failures
 Completed [=====================================================================>---------------------------------]  67% with 0 failures
 Completed [=====================================================================>---------------------------------]  68% with 0 failures
 Completed [======================================================================>--------------------------------]  68% with 0 failures
 Completed [======================================================================>--------------------------------]  69% with 0 failures
 Completed [=======================================================================>-------------------------------]  69% with 0 failures
 Completed [=======================================================================>-------------------------------]  70% with 0 failures
 Completed [========================================================================>------------------------------]  70% with 0 failures
 Completed [========================================================================>------------------------------]  71% with 0 failures
 Completed [=========================================================================>-----------------------------]  71% with 0 failures
 Completed [=========================================================================>-----------------------------]  72% with 0 failures
 Completed [==========================================================================>----------------------------]  72% with 0 failures
 Completed [==========================================================================>----------------------------]  73% with 0 failures
 Completed [===========================================================================>---------------------------]  73% with 0 failures
 Completed [===========================================================================>---------------------------]  74% with 0 failures
 Completed [============================================================================>--------------------------]  74% with 0 failures
 Completed [============================================================================>--------------------------]  75% with 0 failures
 Completed [=============================================================================>-------------------------]  75% with 0 failures
 Completed [=============================================================================>-------------------------]  76% with 0 failures
 Completed [==============================================================================>------------------------]  76% with 0 failures
 Completed [==============================================================================>------------------------]  77% with 0 failures
 Completed [===============================================================================>-----------------------]  77% with 0 failures
 Completed [===============================================================================>-----------------------]  78% with 0 failures
 Completed [================================================================================>----------------------]  78% with 0 failures
 Completed [================================================================================>----------------------]  79% with 0 failures
 Completed [=================================================================================>---------------------]  79% with 0 failures
 Completed [=================================================================================>---------------------]  80% with 0 failures
 Completed [==================================================================================>--------------------]  80% with 0 failures
 Completed [==================================================================================>--------------------]  81% with 0 failures
 Completed [===================================================================================>-------------------]  81% with 0 failures
 Completed [===================================================================================>-------------------]  82% with 0 failures
 Completed [====================================================================================>------------------]  82% with 0 failures
 Completed [====================================================================================>------------------]  83% with 0 failures
 Completed [=====================================================================================>-----------------]  83% with 0 failures
 Completed [=====================================================================================>-----------------]  84% with 0 failures
 Completed [======================================================================================>----------------]  84% with 0 failures
 Completed [======================================================================================>----------------]  85% with 0 failures
 Completed [=======================================================================================>---------------]  85% with 0 failures
 Completed [=======================================================================================>---------------]  86% with 0 failures
 Completed [========================================================================================>--------------]  86% with 0 failures
 Completed [========================================================================================>--------------]  87% with 0 failures
 Completed [=========================================================================================>-------------]  87% with 0 failures
 Completed [=========================================================================================>-------------]  88% with 0 failures
 Completed [==========================================================================================>------------]  88% with 0 failures
 Completed [==========================================================================================>------------]  89% with 0 failures
 Completed [===========================================================================================>-----------]  89% with 0 failures
 Completed [===========================================================================================>-----------]  90% with 0 failures
 Completed [============================================================================================>----------]  90% with 0 failures
 Completed [============================================================================================>----------]  91% with 0 failures
 Completed [=============================================================================================>---------]  91% with 0 failures
 Completed [=============================================================================================>---------]  92% with 0 failures
 Completed [==============================================================================================>--------]  92% with 0 failures
 Completed [==============================================================================================>--------]  93% with 0 failures
 Completed [===============================================================================================>-------]  93% with 0 failures
 Completed [===============================================================================================>-------]  94% with 0 failures
 Completed [================================================================================================>------]  94% with 0 failures
 Completed [================================================================================================>------]  95% with 0 failures
 Completed [=================================================================================================>-----]  95% with 0 failures
 Completed [=================================================================================================>-----]  96% with 0 failures
 Completed [==================================================================================================>----]  96% with 0 failures
 Completed [==================================================================================================>----]  97% with 0 failures
 Completed [===================================================================================================>---]  97% with 0 failures
 Completed [===================================================================================================>---]  98% with 0 failures
 Completed [====================================================================================================>--]  98% with 0 failures
 Completed [====================================================================================================>--]  99% with 0 failures
 Completed [=====================================================================================================>-]  99% with 0 failures
 Completed [======================================================================================================>] 100% with 0 failures
 Completed [=======================================================================================================] 100% with 0 failures
                                                                                                                                         

Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...

 Completed [==>----------------------------------------------------------------------------------------------------]   3% with 0 failures
 Completed [===>---------------------------------------------------------------------------------------------------]   3% with 0 failures
 Completed [===>---------------------------------------------------------------------------------------------------]   4% with 0 failures
 Completed [====>--------------------------------------------------------------------------------------------------]   4% with 0 failures
 Completed [====>--------------------------------------------------------------------------------------------------]   5% with 0 failures
 Completed [=====>-------------------------------------------------------------------------------------------------]   5% with 0 failures
 Completed [=====>-------------------------------------------------------------------------------------------------]   6% with 0 failures
 Completed [======>------------------------------------------------------------------------------------------------]   6% with 0 failures
 Completed [======>------------------------------------------------------------------------------------------------]   7% with 0 failures
 Completed [=======>-----------------------------------------------------------------------------------------------]   7% with 0 failures
 Completed [=======>-----------------------------------------------------------------------------------------------]   8% with 0 failures
 Completed [========>----------------------------------------------------------------------------------------------]   8% with 0 failures
 Completed [========>----------------------------------------------------------------------------------------------]   9% with 0 failures
 Completed [=========>---------------------------------------------------------------------------------------------]   9% with 0 failures
 Completed [=========>---------------------------------------------------------------------------------------------]  10% with 0 failures
 Completed [==========>--------------------------------------------------------------------------------------------]  10% with 0 failures
 Completed [==========>--------------------------------------------------------------------------------------------]  11% with 0 failures
 Completed [===========>-------------------------------------------------------------------------------------------]  11% with 0 failures
 Completed [===========>-------------------------------------------------------------------------------------------]  12% with 0 failures
 Completed [============>------------------------------------------------------------------------------------------]  12% with 0 failures
 Completed [============>------------------------------------------------------------------------------------------]  13% with 0 failures
 Completed [=============>-----------------------------------------------------------------------------------------]  13% with 0 failures
 Completed [=============>-----------------------------------------------------------------------------------------]  14% with 0 failures
 Completed [==============>----------------------------------------------------------------------------------------]  14% with 0 failures
 Completed [==============>----------------------------------------------------------------------------------------]  15% with 0 failures
 Completed [===============>---------------------------------------------------------------------------------------]  15% with 0 failures
 Completed [===============>---------------------------------------------------------------------------------------]  16% with 0 failures
 Completed [================>--------------------------------------------------------------------------------------]  16% with 0 failures
 Completed [================>--------------------------------------------------------------------------------------]  17% with 0 failures
 Completed [=================>-------------------------------------------------------------------------------------]  17% with 0 failures
 Completed [=================>-------------------------------------------------------------------------------------]  18% with 0 failures
 Completed [==================>------------------------------------------------------------------------------------]  18% with 0 failures
 Completed [==================>------------------------------------------------------------------------------------]  19% with 0 failures
 Completed [===================>-----------------------------------------------------------------------------------]  19% with 0 failures
 Completed [===================>-----------------------------------------------------------------------------------]  20% with 0 failures
 Completed [====================>----------------------------------------------------------------------------------]  20% with 0 failures
 Completed [====================>----------------------------------------------------------------------------------]  21% with 0 failures
 Completed [=====================>---------------------------------------------------------------------------------]  21% with 0 failures
 Completed [=====================>---------------------------------------------------------------------------------]  22% with 0 failures
 Completed [======================>--------------------------------------------------------------------------------]  22% with 0 failures
 Completed [======================>--------------------------------------------------------------------------------]  23% with 0 failures
 Completed [=======================>-------------------------------------------------------------------------------]  23% with 0 failures
 Completed [=======================>-------------------------------------------------------------------------------]  24% with 0 failures
 Completed [========================>------------------------------------------------------------------------------]  24% with 0 failures
 Completed [========================>------------------------------------------------------------------------------]  25% with 0 failures
 Completed [=========================>-----------------------------------------------------------------------------]  25% with 0 failures
 Completed [=========================>-----------------------------------------------------------------------------]  26% with 0 failures
 Completed [==========================>----------------------------------------------------------------------------]  26% with 0 failures
 Completed [==========================>----------------------------------------------------------------------------]  27% with 0 failures
 Completed [===========================>---------------------------------------------------------------------------]  27% with 0 failures
 Completed [===========================>---------------------------------------------------------------------------]  28% with 0 failures
 Completed [============================>--------------------------------------------------------------------------]  28% with 0 failures
 Completed [============================>--------------------------------------------------------------------------]  29% with 0 failures
 Completed [=============================>-------------------------------------------------------------------------]  29% with 0 failures
 Completed [=============================>-------------------------------------------------------------------------]  30% with 0 failures
 Completed [==============================>------------------------------------------------------------------------]  30% with 0 failures
 Completed [==============================>------------------------------------------------------------------------]  31% with 0 failures
 Completed [===============================>-----------------------------------------------------------------------]  31% with 0 failures
 Completed [===============================>-----------------------------------------------------------------------]  32% with 0 failures
 Completed [================================>----------------------------------------------------------------------]  32% with 0 failures
 Completed [================================>----------------------------------------------------------------------]  33% with 0 failures
 Completed [=================================>---------------------------------------------------------------------]  33% with 0 failures
 Completed [==================================>--------------------------------------------------------------------]  34% with 0 failures
 Completed [===================================>-------------------------------------------------------------------]  35% with 0 failures
 Completed [====================================>------------------------------------------------------------------]  35% with 0 failures
 Completed [====================================>------------------------------------------------------------------]  36% with 0 failures
 Completed [=====================================>-----------------------------------------------------------------]  36% with 0 failures
 Completed [=====================================>-----------------------------------------------------------------]  37% with 0 failures
 Completed [======================================>----------------------------------------------------------------]  37% with 0 failures
 Completed [======================================>----------------------------------------------------------------]  38% with 0 failures
 Completed [=======================================>---------------------------------------------------------------]  38% with 0 failures
 Completed [=======================================>---------------------------------------------------------------]  39% with 0 failures
 Completed [========================================>--------------------------------------------------------------]  39% with 0 failures
 Completed [========================================>--------------------------------------------------------------]  40% with 0 failures
 Completed [=========================================>-------------------------------------------------------------]  40% with 0 failures
 Completed [=========================================>-------------------------------------------------------------]  41% with 0 failures
 Completed [==========================================>------------------------------------------------------------]  41% with 0 failures
 Completed [==========================================>------------------------------------------------------------]  42% with 0 failures
 Completed [===========================================>-----------------------------------------------------------]  42% with 0 failures
 Completed [===========================================>-----------------------------------------------------------]  43% with 0 failures
 Completed [============================================>----------------------------------------------------------]  43% with 0 failures
 Completed [============================================>----------------------------------------------------------]  44% with 0 failures
 Completed [=============================================>---------------------------------------------------------]  44% with 0 failures
 Completed [=============================================>---------------------------------------------------------]  45% with 0 failures
 Completed [==============================================>--------------------------------------------------------]  45% with 0 failures
 Completed [==============================================>--------------------------------------------------------]  46% with 0 failures
 Completed [===============================================>-------------------------------------------------------]  46% with 0 failures
 Completed [===============================================>-------------------------------------------------------]  47% with 0 failures
 Completed [================================================>------------------------------------------------------]  47% with 0 failures
 Completed [================================================>------------------------------------------------------]  48% with 0 failures
 Completed [=================================================>-----------------------------------------------------]  48% with 0 failures
 Completed [=================================================>-----------------------------------------------------]  49% with 0 failures
 Completed [==================================================>----------------------------------------------------]  49% with 0 failures
 Completed [==================================================>----------------------------------------------------]  50% with 0 failures
 Completed [===================================================>---------------------------------------------------]  50% with 0 failures
 Completed [===================================================>---------------------------------------------------]  51% with 0 failures
 Completed [====================================================>--------------------------------------------------]  51% with 0 failures
 Completed [====================================================>--------------------------------------------------]  52% with 0 failures
 Completed [=====================================================>-------------------------------------------------]  52% with 0 failures
 Completed [=====================================================>-------------------------------------------------]  53% with 0 failures
 Completed [======================================================>------------------------------------------------]  53% with 0 failures
 Completed [======================================================>------------------------------------------------]  54% with 0 failures
 Completed [=======================================================>-----------------------------------------------]  54% with 0 failures
 Completed [=======================================================>-----------------------------------------------]  55% with 0 failures
 Completed [========================================================>----------------------------------------------]  55% with 0 failures
 Completed [========================================================>----------------------------------------------]  56% with 0 failures
 Completed [=========================================================>---------------------------------------------]  56% with 0 failures
 Completed [=========================================================>---------------------------------------------]  57% with 0 failures
 Completed [==========================================================>--------------------------------------------]  57% with 0 failures
 Completed [==========================================================>--------------------------------------------]  58% with 0 failures
 Completed [===========================================================>-------------------------------------------]  58% with 0 failures
 Completed [===========================================================>-------------------------------------------]  59% with 0 failures
 Completed [============================================================>------------------------------------------]  59% with 0 failures
 Completed [============================================================>------------------------------------------]  60% with 0 failures
 Completed [=============================================================>-----------------------------------------]  60% with 0 failures
 Completed [=============================================================>-----------------------------------------]  61% with 0 failures
 Completed [==============================================================>----------------------------------------]  61% with 0 failures
 Completed [==============================================================>----------------------------------------]  62% with 0 failures
 Completed [===============================================================>---------------------------------------]  62% with 0 failures
 Completed [===============================================================>---------------------------------------]  63% with 0 failures
 Completed [================================================================>--------------------------------------]  63% with 0 failures
 Completed [================================================================>--------------------------------------]  64% with 0 failures
 Completed [=================================================================>-------------------------------------]  64% with 0 failures
 Completed [=================================================================>-------------------------------------]  65% with 0 failures
 Completed [==================================================================>------------------------------------]  65% with 0 failures
 Completed [===================================================================>-----------------------------------]  66% with 0 failures
 Completed [====================================================================>----------------------------------]  67% with 0 failures
 Completed [=====================================================================>---------------------------------]  67% with 0 failures
 Completed [=====================================================================>---------------------------------]  68% with 0 failures
 Completed [======================================================================>--------------------------------]  68% with 0 failures
 Completed [======================================================================>--------------------------------]  69% with 0 failures
 Completed [=======================================================================>-------------------------------]  69% with 0 failures
 Completed [=======================================================================>-------------------------------]  70% with 0 failures
 Completed [========================================================================>------------------------------]  70% with 0 failures
 Completed [========================================================================>------------------------------]  71% with 0 failures
 Completed [=========================================================================>-----------------------------]  71% with 0 failures
 Completed [=========================================================================>-----------------------------]  72% with 0 failures
 Completed [==========================================================================>----------------------------]  72% with 0 failures
 Completed [==========================================================================>----------------------------]  73% with 0 failures
 Completed [===========================================================================>---------------------------]  73% with 0 failures
 Completed [===========================================================================>---------------------------]  74% with 0 failures
 Completed [============================================================================>--------------------------]  74% with 0 failures
 Completed [============================================================================>--------------------------]  75% with 0 failures
 Completed [=============================================================================>-------------------------]  75% with 0 failures
 Completed [=============================================================================>-------------------------]  76% with 0 failures
 Completed [==============================================================================>------------------------]  76% with 0 failures
 Completed [==============================================================================>------------------------]  77% with 0 failures
 Completed [===============================================================================>-----------------------]  77% with 0 failures
 Completed [===============================================================================>-----------------------]  78% with 0 failures
 Completed [================================================================================>----------------------]  78% with 0 failures
 Completed [================================================================================>----------------------]  79% with 0 failures
 Completed [=================================================================================>---------------------]  79% with 0 failures
 Completed [=================================================================================>---------------------]  80% with 0 failures
 Completed [==================================================================================>--------------------]  80% with 0 failures
 Completed [==================================================================================>--------------------]  81% with 0 failures
 Completed [===================================================================================>-------------------]  81% with 0 failures
 Completed [===================================================================================>-------------------]  82% with 0 failures
 Completed [====================================================================================>------------------]  82% with 0 failures
 Completed [====================================================================================>------------------]  83% with 0 failures
 Completed [=====================================================================================>-----------------]  83% with 0 failures
 Completed [=====================================================================================>-----------------]  84% with 0 failures
 Completed [======================================================================================>----------------]  84% with 0 failures
 Completed [======================================================================================>----------------]  85% with 0 failures
 Completed [=======================================================================================>---------------]  85% with 0 failures
 Completed [=======================================================================================>---------------]  86% with 0 failures
 Completed [========================================================================================>--------------]  86% with 0 failures
 Completed [========================================================================================>--------------]  87% with 0 failures
 Completed [=========================================================================================>-------------]  87% with 0 failures
 Completed [=========================================================================================>-------------]  88% with 0 failures
 Completed [==========================================================================================>------------]  88% with 0 failures
 Completed [==========================================================================================>------------]  89% with 0 failures
 Completed [===========================================================================================>-----------]  89% with 0 failures
 Completed [===========================================================================================>-----------]  90% with 0 failures
 Completed [============================================================================================>----------]  90% with 0 failures
 Completed [============================================================================================>----------]  91% with 0 failures
 Completed [=============================================================================================>---------]  91% with 0 failures
 Completed [=============================================================================================>---------]  92% with 0 failures
 Completed [==============================================================================================>--------]  92% with 0 failures
 Completed [==============================================================================================>--------]  93% with 0 failures
 Completed [===============================================================================================>-------]  93% with 0 failures
 Completed [===============================================================================================>-------]  94% with 0 failures
 Completed [================================================================================================>------]  94% with 0 failures
 Completed [================================================================================================>------]  95% with 0 failures
 Completed [=================================================================================================>-----]  95% with 0 failures
 Completed [=================================================================================================>-----]  96% with 0 failures
 Completed [==================================================================================================>----]  96% with 0 failures
 Completed [==================================================================================================>----]  97% with 0 failures
 Completed [===================================================================================================>---]  97% with 0 failures
 Completed [===================================================================================================>---]  98% with 0 failures
 Completed [====================================================================================================>--]  98% with 0 failures
 Completed [====================================================================================================>--]  99% with 0 failures
 Completed [=====================================================================================================>-]  99% with 0 failures
 Completed [======================================================================================================>] 100% with 0 failures
 Completed [=======================================================================================================] 100% with 0 failures
                                                                                                                                         

Done!
Calculating cluster 1

 Completed [======>------------------------------------------------------------------------------------------------]   7% with 0 failures
 Completed [=======>-----------------------------------------------------------------------------------------------]   7% with 0 failures
 Completed [=======>-----------------------------------------------------------------------------------------------]   8% with 0 failures
 Completed [========>----------------------------------------------------------------------------------------------]   8% with 0 failures
 Completed [========>----------------------------------------------------------------------------------------------]   9% with 0 failures
 Completed [=========>---------------------------------------------------------------------------------------------]   9% with 0 failures
 Completed [=========>---------------------------------------------------------------------------------------------]  10% with 0 failures
 Completed [==========>--------------------------------------------------------------------------------------------]  10% with 0 failures
 Completed [==========>--------------------------------------------------------------------------------------------]  11% with 0 failures
 Completed [===========>-------------------------------------------------------------------------------------------]  11% with 0 failures
 Completed [===========>-------------------------------------------------------------------------------------------]  12% with 0 failures
 Completed [============>------------------------------------------------------------------------------------------]  12% with 0 failures
 Completed [============>------------------------------------------------------------------------------------------]  13% with 0 failures
 Completed [=============>-----------------------------------------------------------------------------------------]  13% with 0 failures
 Completed [=============>-----------------------------------------------------------------------------------------]  14% with 0 failures
 Completed [==============>----------------------------------------------------------------------------------------]  14% with 0 failures
 Completed [==============>----------------------------------------------------------------------------------------]  15% with 0 failures
 Completed [===============>---------------------------------------------------------------------------------------]  15% with 0 failures
 Completed [===============>---------------------------------------------------------------------------------------]  16% with 0 failures
 Completed [================>--------------------------------------------------------------------------------------]  16% with 0 failures
 Completed [================>--------------------------------------------------------------------------------------]  17% with 0 failures
 Completed [=================>-------------------------------------------------------------------------------------]  17% with 0 failures
 Completed [=================>-------------------------------------------------------------------------------------]  18% with 0 failures
 Completed [==================>------------------------------------------------------------------------------------]  18% with 0 failures
 Completed [==================>------------------------------------------------------------------------------------]  19% with 0 failures
 Completed [===================>-----------------------------------------------------------------------------------]  19% with 0 failures
 Completed [===================>-----------------------------------------------------------------------------------]  20% with 0 failures
 Completed [====================>----------------------------------------------------------------------------------]  20% with 0 failures
 Completed [====================>----------------------------------------------------------------------------------]  21% with 0 failures
 Completed [=====================>---------------------------------------------------------------------------------]  21% with 0 failures
 Completed [=====================>---------------------------------------------------------------------------------]  22% with 0 failures
 Completed [======================>--------------------------------------------------------------------------------]  22% with 0 failures
 Completed [======================>--------------------------------------------------------------------------------]  23% with 0 failures
 Completed [=======================>-------------------------------------------------------------------------------]  23% with 0 failures
 Completed [=======================>-------------------------------------------------------------------------------]  24% with 0 failures
 Completed [========================>------------------------------------------------------------------------------]  24% with 0 failures
 Completed [========================>------------------------------------------------------------------------------]  25% with 0 failures
 Completed [=========================>-----------------------------------------------------------------------------]  25% with 0 failures
 Completed [=========================>-----------------------------------------------------------------------------]  26% with 0 failures
 Completed [==========================>----------------------------------------------------------------------------]  26% with 0 failures
 Completed [==========================>----------------------------------------------------------------------------]  27% with 0 failures
 Completed [===========================>---------------------------------------------------------------------------]  27% with 0 failures
 Completed [===========================>---------------------------------------------------------------------------]  28% with 0 failures
 Completed [============================>--------------------------------------------------------------------------]  28% with 0 failures
 Completed [============================>--------------------------------------------------------------------------]  29% with 0 failures
 Completed [=============================>-------------------------------------------------------------------------]  29% with 0 failures
 Completed [=============================>-------------------------------------------------------------------------]  30% with 0 failures
 Completed [==============================>------------------------------------------------------------------------]  30% with 0 failures
 Completed [==============================>------------------------------------------------------------------------]  31% with 0 failures
 Completed [===============================>-----------------------------------------------------------------------]  31% with 0 failures
 Completed [================================>----------------------------------------------------------------------]  32% with 0 failures
 Completed [=================================>---------------------------------------------------------------------]  33% with 0 failures
 Completed [==================================>--------------------------------------------------------------------]  34% with 0 failures
 Completed [===================================>-------------------------------------------------------------------]  35% with 0 failures
 Completed [====================================>------------------------------------------------------------------]  35% with 0 failures
 Completed [====================================>------------------------------------------------------------------]  36% with 0 failures
 Completed [=====================================>-----------------------------------------------------------------]  36% with 0 failures
 Completed [=====================================>-----------------------------------------------------------------]  37% with 0 failures
 Completed [======================================>----------------------------------------------------------------]  37% with 0 failures
 Completed [======================================>----------------------------------------------------------------]  38% with 0 failures
 Completed [=======================================>---------------------------------------------------------------]  38% with 0 failures
 Completed [=======================================>---------------------------------------------------------------]  39% with 0 failures
 Completed [========================================>--------------------------------------------------------------]  39% with 0 failures
 Completed [========================================>--------------------------------------------------------------]  40% with 0 failures
 Completed [=========================================>-------------------------------------------------------------]  40% with 0 failures
 Completed [=========================================>-------------------------------------------------------------]  41% with 0 failures
 Completed [==========================================>------------------------------------------------------------]  41% with 0 failures
 Completed [==========================================>------------------------------------------------------------]  42% with 0 failures
 Completed [===========================================>-----------------------------------------------------------]  42% with 0 failures
 Completed [===========================================>-----------------------------------------------------------]  43% with 0 failures
 Completed [============================================>----------------------------------------------------------]  43% with 0 failures
 Completed [============================================>----------------------------------------------------------]  44% with 0 failures
 Completed [=============================================>---------------------------------------------------------]  44% with 0 failures
 Completed [=============================================>---------------------------------------------------------]  45% with 0 failures
 Completed [==============================================>--------------------------------------------------------]  45% with 0 failures
 Completed [==============================================>--------------------------------------------------------]  46% with 0 failures
 Completed [===============================================>-------------------------------------------------------]  46% with 0 failures
 Completed [===============================================>-------------------------------------------------------]  47% with 0 failures
 Completed [================================================>------------------------------------------------------]  47% with 0 failures
 Completed [================================================>------------------------------------------------------]  48% with 0 failures
 Completed [=================================================>-----------------------------------------------------]  48% with 0 failures
 Completed [=================================================>-----------------------------------------------------]  49% with 0 failures
 Completed [==================================================>----------------------------------------------------]  49% with 0 failures
 Completed [==================================================>----------------------------------------------------]  50% with 0 failures
 Completed [===================================================>---------------------------------------------------]  50% with 0 failures
 Completed [===================================================>---------------------------------------------------]  51% with 0 failures
 Completed [====================================================>--------------------------------------------------]  51% with 0 failures
 Completed [====================================================>--------------------------------------------------]  52% with 0 failures
 Completed [=====================================================>-------------------------------------------------]  52% with 0 failures
 Completed [=====================================================>-------------------------------------------------]  53% with 0 failures
 Completed [======================================================>------------------------------------------------]  53% with 0 failures
 Completed [======================================================>------------------------------------------------]  54% with 0 failures
 Completed [=======================================================>-----------------------------------------------]  54% with 0 failures
 Completed [=======================================================>-----------------------------------------------]  55% with 0 failures
 Completed [========================================================>----------------------------------------------]  55% with 0 failures
 Completed [========================================================>----------------------------------------------]  56% with 0 failures
 Completed [=========================================================>---------------------------------------------]  56% with 0 failures
 Completed [=========================================================>---------------------------------------------]  57% with 0 failures
 Completed [==========================================================>--------------------------------------------]  57% with 0 failures
 Completed [==========================================================>--------------------------------------------]  58% with 0 failures
 Completed [===========================================================>-------------------------------------------]  58% with 0 failures
 Completed [===========================================================>-------------------------------------------]  59% with 0 failures
 Completed [============================================================>------------------------------------------]  59% with 0 failures
 Completed [============================================================>------------------------------------------]  60% with 0 failures
 Completed [=============================================================>-----------------------------------------]  60% with 0 failures
 Completed [=============================================================>-----------------------------------------]  61% with 0 failures
 Completed [==============================================================>----------------------------------------]  61% with 0 failures
 Completed [==============================================================>----------------------------------------]  62% with 0 failures
 Completed [===============================================================>---------------------------------------]  62% with 0 failures
 Completed [===============================================================>---------------------------------------]  63% with 0 failures
 Completed [================================================================>--------------------------------------]  63% with 0 failures
 Completed [================================================================>--------------------------------------]  64% with 0 failures
 Completed [=================================================================>-------------------------------------]  64% with 0 failures
 Completed [=================================================================>-------------------------------------]  65% with 0 failures
 Completed [==================================================================>------------------------------------]  65% with 0 failures
 Completed [===================================================================>-----------------------------------]  66% with 0 failures
 Completed [====================================================================>----------------------------------]  67% with 0 failures
 Completed [=====================================================================>---------------------------------]  68% with 0 failures
 Completed [======================================================================>--------------------------------]  69% with 0 failures
 Completed [=======================================================================>-------------------------------]  69% with 0 failures
 Completed [=======================================================================>-------------------------------]  70% with 0 failures
 Completed [========================================================================>------------------------------]  70% with 0 failures
 Completed [========================================================================>------------------------------]  71% with 0 failures
 Completed [=========================================================================>-----------------------------]  71% with 0 failures
 Completed [=========================================================================>-----------------------------]  72% with 0 failures
 Completed [==========================================================================>----------------------------]  72% with 0 failures
 Completed [==========================================================================>----------------------------]  73% with 0 failures
 Completed [===========================================================================>---------------------------]  73% with 0 failures
 Completed [===========================================================================>---------------------------]  74% with 0 failures
 Completed [============================================================================>--------------------------]  74% with 0 failures
 Completed [============================================================================>--------------------------]  75% with 0 failures
 Completed [=============================================================================>-------------------------]  75% with 0 failures
 Completed [=============================================================================>-------------------------]  76% with 0 failures
 Completed [==============================================================================>------------------------]  76% with 0 failures
 Completed [==============================================================================>------------------------]  77% with 0 failures
 Completed [===============================================================================>-----------------------]  77% with 0 failures
 Completed [===============================================================================>-----------------------]  78% with 0 failures
 Completed [================================================================================>----------------------]  78% with 0 failures
 Completed [================================================================================>----------------------]  79% with 0 failures
 Completed [=================================================================================>---------------------]  79% with 0 failures
 Completed [=================================================================================>---------------------]  80% with 0 failures
 Completed [==================================================================================>--------------------]  80% with 0 failures
 Completed [==================================================================================>--------------------]  81% with 0 failures
 Completed [===================================================================================>-------------------]  81% with 0 failures
 Completed [===================================================================================>-------------------]  82% with 0 failures
 Completed [====================================================================================>------------------]  82% with 0 failures
 Completed [====================================================================================>------------------]  83% with 0 failures
 Completed [=====================================================================================>-----------------]  83% with 0 failures
 Completed [=====================================================================================>-----------------]  84% with 0 failures
 Completed [======================================================================================>----------------]  84% with 0 failures
 Completed [======================================================================================>----------------]  85% with 0 failures
 Completed [=======================================================================================>---------------]  85% with 0 failures
 Completed [=======================================================================================>---------------]  86% with 0 failures
 Completed [========================================================================================>--------------]  86% with 0 failures
 Completed [========================================================================================>--------------]  87% with 0 failures
 Completed [=========================================================================================>-------------]  87% with 0 failures
 Completed [=========================================================================================>-------------]  88% with 0 failures
 Completed [==========================================================================================>------------]  88% with 0 failures
 Completed [==========================================================================================>------------]  89% with 0 failures
 Completed [===========================================================================================>-----------]  89% with 0 failures
 Completed [===========================================================================================>-----------]  90% with 0 failures
 Completed [============================================================================================>----------]  90% with 0 failures
 Completed [============================================================================================>----------]  91% with 0 failures
 Completed [=============================================================================================>---------]  91% with 0 failures
 Completed [=============================================================================================>---------]  92% with 0 failures
 Completed [==============================================================================================>--------]  92% with 0 failures
 Completed [==============================================================================================>--------]  93% with 0 failures
 Completed [===============================================================================================>-------]  93% with 0 failures
 Completed [===============================================================================================>-------]  94% with 0 failures
 Completed [================================================================================================>------]  94% with 0 failures
 Completed [================================================================================================>------]  95% with 0 failures
 Completed [=================================================================================================>-----]  95% with 0 failures
 Completed [=================================================================================================>-----]  96% with 0 failures
 Completed [==================================================================================================>----]  96% with 0 failures
 Completed [==================================================================================================>----]  97% with 0 failures
 Completed [===================================================================================================>---]  97% with 0 failures
 Completed [===================================================================================================>---]  98% with 0 failures
 Completed [====================================================================================================>--]  98% with 0 failures
 Completed [====================================================================================================>--]  99% with 0 failures
 Completed [=====================================================================================================>-]  99% with 0 failures
 Completed [=====================================================================================================>-] 100% with 0 failures
 Completed [======================================================================================================>] 100% with 0 failures
 Completed [=======================================================================================================] 100% with 0 failures
                                                                                                                                         

Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...

 Completed [======>------------------------------------------------------------------------------------------------]   7% with 0 failures
 Completed [=======>-----------------------------------------------------------------------------------------------]   7% with 0 failures
 Completed [=======>-----------------------------------------------------------------------------------------------]   8% with 0 failures
 Completed [========>----------------------------------------------------------------------------------------------]   8% with 0 failures
 Completed [========>----------------------------------------------------------------------------------------------]   9% with 0 failures
 Completed [=========>---------------------------------------------------------------------------------------------]   9% with 0 failures
 Completed [=========>---------------------------------------------------------------------------------------------]  10% with 0 failures
 Completed [==========>--------------------------------------------------------------------------------------------]  10% with 0 failures
 Completed [==========>--------------------------------------------------------------------------------------------]  11% with 0 failures
 Completed [===========>-------------------------------------------------------------------------------------------]  11% with 0 failures
 Completed [===========>-------------------------------------------------------------------------------------------]  12% with 0 failures
 Completed [============>------------------------------------------------------------------------------------------]  12% with 0 failures
 Completed [============>------------------------------------------------------------------------------------------]  13% with 0 failures
 Completed [=============>-----------------------------------------------------------------------------------------]  13% with 0 failures
 Completed [=============>-----------------------------------------------------------------------------------------]  14% with 0 failures
 Completed [==============>----------------------------------------------------------------------------------------]  14% with 0 failures
 Completed [==============>----------------------------------------------------------------------------------------]  15% with 0 failures
 Completed [===============>---------------------------------------------------------------------------------------]  15% with 0 failures
 Completed [===============>---------------------------------------------------------------------------------------]  16% with 0 failures
 Completed [================>--------------------------------------------------------------------------------------]  16% with 0 failures
 Completed [================>--------------------------------------------------------------------------------------]  17% with 0 failures
 Completed [=================>-------------------------------------------------------------------------------------]  17% with 0 failures
 Completed [=================>-------------------------------------------------------------------------------------]  18% with 0 failures
 Completed [==================>------------------------------------------------------------------------------------]  18% with 0 failures
 Completed [==================>------------------------------------------------------------------------------------]  19% with 0 failures
 Completed [===================>-----------------------------------------------------------------------------------]  19% with 0 failures
 Completed [===================>-----------------------------------------------------------------------------------]  20% with 0 failures
 Completed [====================>----------------------------------------------------------------------------------]  20% with 0 failures
 Completed [====================>----------------------------------------------------------------------------------]  21% with 0 failures
 Completed [=====================>---------------------------------------------------------------------------------]  21% with 0 failures
 Completed [=====================>---------------------------------------------------------------------------------]  22% with 0 failures
 Completed [======================>--------------------------------------------------------------------------------]  22% with 0 failures
 Completed [======================>--------------------------------------------------------------------------------]  23% with 0 failures
 Completed [=======================>-------------------------------------------------------------------------------]  23% with 0 failures
 Completed [=======================>-------------------------------------------------------------------------------]  24% with 0 failures
 Completed [========================>------------------------------------------------------------------------------]  24% with 0 failures
 Completed [========================>------------------------------------------------------------------------------]  25% with 0 failures
 Completed [=========================>-----------------------------------------------------------------------------]  25% with 0 failures
 Completed [=========================>-----------------------------------------------------------------------------]  26% with 0 failures
 Completed [==========================>----------------------------------------------------------------------------]  26% with 0 failures
 Completed [==========================>----------------------------------------------------------------------------]  27% with 0 failures
 Completed [===========================>---------------------------------------------------------------------------]  27% with 0 failures
 Completed [===========================>---------------------------------------------------------------------------]  28% with 0 failures
 Completed [============================>--------------------------------------------------------------------------]  28% with 0 failures
 Completed [============================>--------------------------------------------------------------------------]  29% with 0 failures
 Completed [=============================>-------------------------------------------------------------------------]  29% with 0 failures
 Completed [=============================>-------------------------------------------------------------------------]  30% with 0 failures
 Completed [==============================>------------------------------------------------------------------------]  30% with 0 failures
 Completed [==============================>------------------------------------------------------------------------]  31% with 0 failures
 Completed [===============================>-----------------------------------------------------------------------]  31% with 0 failures
 Completed [================================>----------------------------------------------------------------------]  32% with 0 failures
 Completed [=================================>---------------------------------------------------------------------]  33% with 0 failures
 Completed [==================================>--------------------------------------------------------------------]  34% with 0 failures
 Completed [===================================>-------------------------------------------------------------------]  35% with 0 failures
 Completed [====================================>------------------------------------------------------------------]  35% with 0 failures
 Completed [====================================>------------------------------------------------------------------]  36% with 0 failures
 Completed [=====================================>-----------------------------------------------------------------]  36% with 0 failures
 Completed [=====================================>-----------------------------------------------------------------]  37% with 0 failures
 Completed [======================================>----------------------------------------------------------------]  37% with 0 failures
 Completed [======================================>----------------------------------------------------------------]  38% with 0 failures
 Completed [=======================================>---------------------------------------------------------------]  38% with 0 failures
 Completed [=======================================>---------------------------------------------------------------]  39% with 0 failures
 Completed [========================================>--------------------------------------------------------------]  39% with 0 failures
 Completed [========================================>--------------------------------------------------------------]  40% with 0 failures
 Completed [=========================================>-------------------------------------------------------------]  40% with 0 failures
 Completed [=========================================>-------------------------------------------------------------]  41% with 0 failures
 Completed [==========================================>------------------------------------------------------------]  41% with 0 failures
 Completed [==========================================>------------------------------------------------------------]  42% with 0 failures
 Completed [===========================================>-----------------------------------------------------------]  42% with 0 failures
 Completed [===========================================>-----------------------------------------------------------]  43% with 0 failures
 Completed [============================================>----------------------------------------------------------]  43% with 0 failures
 Completed [============================================>----------------------------------------------------------]  44% with 0 failures
 Completed [=============================================>---------------------------------------------------------]  44% with 0 failures
 Completed [=============================================>---------------------------------------------------------]  45% with 0 failures
 Completed [==============================================>--------------------------------------------------------]  45% with 0 failures
 Completed [==============================================>--------------------------------------------------------]  46% with 0 failures
 Completed [===============================================>-------------------------------------------------------]  46% with 0 failures
 Completed [===============================================>-------------------------------------------------------]  47% with 0 failures
 Completed [================================================>------------------------------------------------------]  47% with 0 failures
 Completed [================================================>------------------------------------------------------]  48% with 0 failures
 Completed [=================================================>-----------------------------------------------------]  48% with 0 failures
 Completed [=================================================>-----------------------------------------------------]  49% with 0 failures
 Completed [==================================================>----------------------------------------------------]  49% with 0 failures
 Completed [==================================================>----------------------------------------------------]  50% with 0 failures
 Completed [===================================================>---------------------------------------------------]  50% with 0 failures
 Completed [===================================================>---------------------------------------------------]  51% with 0 failures
 Completed [====================================================>--------------------------------------------------]  51% with 0 failures
 Completed [====================================================>--------------------------------------------------]  52% with 0 failures
 Completed [=====================================================>-------------------------------------------------]  52% with 0 failures
 Completed [=====================================================>-------------------------------------------------]  53% with 0 failures
 Completed [======================================================>------------------------------------------------]  53% with 0 failures
 Completed [======================================================>------------------------------------------------]  54% with 0 failures
 Completed [=======================================================>-----------------------------------------------]  54% with 0 failures
 Completed [=======================================================>-----------------------------------------------]  55% with 0 failures
 Completed [========================================================>----------------------------------------------]  55% with 0 failures
 Completed [========================================================>----------------------------------------------]  56% with 0 failures
 Completed [=========================================================>---------------------------------------------]  56% with 0 failures
 Completed [=========================================================>---------------------------------------------]  57% with 0 failures
 Completed [==========================================================>--------------------------------------------]  57% with 0 failures
 Completed [==========================================================>--------------------------------------------]  58% with 0 failures
 Completed [===========================================================>-------------------------------------------]  58% with 0 failures
 Completed [===========================================================>-------------------------------------------]  59% with 0 failures
 Completed [============================================================>------------------------------------------]  59% with 0 failures
 Completed [============================================================>------------------------------------------]  60% with 0 failures
 Completed [=============================================================>-----------------------------------------]  60% with 0 failures
 Completed [=============================================================>-----------------------------------------]  61% with 0 failures
 Completed [==============================================================>----------------------------------------]  61% with 0 failures
 Completed [==============================================================>----------------------------------------]  62% with 0 failures
 Completed [===============================================================>---------------------------------------]  62% with 0 failures
 Completed [===============================================================>---------------------------------------]  63% with 0 failures
 Completed [================================================================>--------------------------------------]  63% with 0 failures
 Completed [================================================================>--------------------------------------]  64% with 0 failures
 Completed [=================================================================>-------------------------------------]  64% with 0 failures
 Completed [=================================================================>-------------------------------------]  65% with 0 failures
 Completed [==================================================================>------------------------------------]  65% with 0 failures
 Completed [===================================================================>-----------------------------------]  66% with 0 failures
 Completed [====================================================================>----------------------------------]  67% with 0 failures
 Completed [=====================================================================>---------------------------------]  68% with 0 failures
 Completed [======================================================================>--------------------------------]  69% with 0 failures
 Completed [=======================================================================>-------------------------------]  69% with 0 failures
 Completed [=======================================================================>-------------------------------]  70% with 0 failures
 Completed [========================================================================>------------------------------]  70% with 0 failures
 Completed [========================================================================>------------------------------]  71% with 0 failures
 Completed [=========================================================================>-----------------------------]  71% with 0 failures
 Completed [=========================================================================>-----------------------------]  72% with 0 failures
 Completed [==========================================================================>----------------------------]  72% with 0 failures
 Completed [==========================================================================>----------------------------]  73% with 0 failures
 Completed [===========================================================================>---------------------------]  73% with 0 failures
 Completed [===========================================================================>---------------------------]  74% with 0 failures
 Completed [============================================================================>--------------------------]  74% with 0 failures
 Completed [============================================================================>--------------------------]  75% with 0 failures
 Completed [=============================================================================>-------------------------]  75% with 0 failures
 Completed [=============================================================================>-------------------------]  76% with 0 failures
 Completed [==============================================================================>------------------------]  76% with 0 failures
 Completed [==============================================================================>------------------------]  77% with 0 failures
 Completed [===============================================================================>-----------------------]  77% with 0 failures
 Completed [===============================================================================>-----------------------]  78% with 0 failures
 Completed [================================================================================>----------------------]  78% with 0 failures
 Completed [================================================================================>----------------------]  79% with 0 failures
 Completed [=================================================================================>---------------------]  79% with 0 failures
 Completed [=================================================================================>---------------------]  80% with 0 failures
 Completed [==================================================================================>--------------------]  80% with 0 failures
 Completed [==================================================================================>--------------------]  81% with 0 failures
 Completed [===================================================================================>-------------------]  81% with 0 failures
 Completed [===================================================================================>-------------------]  82% with 0 failures
 Completed [====================================================================================>------------------]  82% with 0 failures
 Completed [====================================================================================>------------------]  83% with 0 failures
 Completed [=====================================================================================>-----------------]  83% with 0 failures
 Completed [=====================================================================================>-----------------]  84% with 0 failures
 Completed [======================================================================================>----------------]  84% with 0 failures
 Completed [======================================================================================>----------------]  85% with 0 failures
 Completed [=======================================================================================>---------------]  85% with 0 failures
 Completed [=======================================================================================>---------------]  86% with 0 failures
 Completed [========================================================================================>--------------]  86% with 0 failures
 Completed [========================================================================================>--------------]  87% with 0 failures
 Completed [=========================================================================================>-------------]  87% with 0 failures
 Completed [=========================================================================================>-------------]  88% with 0 failures
 Completed [==========================================================================================>------------]  88% with 0 failures
 Completed [==========================================================================================>------------]  89% with 0 failures
 Completed [===========================================================================================>-----------]  89% with 0 failures
 Completed [===========================================================================================>-----------]  90% with 0 failures
 Completed [============================================================================================>----------]  90% with 0 failures
 Completed [============================================================================================>----------]  91% with 0 failures
 Completed [=============================================================================================>---------]  91% with 0 failures
 Completed [=============================================================================================>---------]  92% with 0 failures
 Completed [==============================================================================================>--------]  92% with 0 failures
 Completed [==============================================================================================>--------]  93% with 0 failures
 Completed [===============================================================================================>-------]  93% with 0 failures
 Completed [===============================================================================================>-------]  94% with 0 failures
 Completed [================================================================================================>------]  94% with 0 failures
 Completed [================================================================================================>------]  95% with 0 failures
 Completed [=================================================================================================>-----]  95% with 0 failures
 Completed [=================================================================================================>-----]  96% with 0 failures
 Completed [==================================================================================================>----]  96% with 0 failures
 Completed [==================================================================================================>----]  97% with 0 failures
 Completed [===================================================================================================>---]  97% with 0 failures
 Completed [===================================================================================================>---]  98% with 0 failures
 Completed [====================================================================================================>--]  98% with 0 failures
 Completed [====================================================================================================>--]  99% with 0 failures
 Completed [=====================================================================================================>-]  99% with 0 failures
 Completed [=====================================================================================================>-] 100% with 0 failures
 Completed [======================================================================================================>] 100% with 0 failures
 Completed [=======================================================================================================] 100% with 0 failures
                                                                                                                                         

Done!
Calculating cluster 2

 Completed [=>-----------------------------------------------------------------------------------------------------]   2% with 0 failures
 Completed [==>----------------------------------------------------------------------------------------------------]   2% with 0 failures
 Completed [==>----------------------------------------------------------------------------------------------------]   3% with 0 failures
 Completed [===>---------------------------------------------------------------------------------------------------]   3% with 0 failures
 Completed [===>---------------------------------------------------------------------------------------------------]   4% with 0 failures
 Completed [====>--------------------------------------------------------------------------------------------------]   4% with 0 failures
 Completed [====>--------------------------------------------------------------------------------------------------]   5% with 0 failures
 Completed [=====>-------------------------------------------------------------------------------------------------]   5% with 0 failures
 Completed [=====>-------------------------------------------------------------------------------------------------]   6% with 0 failures
 Completed [======>------------------------------------------------------------------------------------------------]   6% with 0 failures
 Completed [======>------------------------------------------------------------------------------------------------]   7% with 0 failures
 Completed [=======>-----------------------------------------------------------------------------------------------]   7% with 0 failures
 Completed [=======>-----------------------------------------------------------------------------------------------]   8% with 0 failures
 Completed [========>----------------------------------------------------------------------------------------------]   8% with 0 failures
 Completed [========>----------------------------------------------------------------------------------------------]   9% with 0 failures
 Completed [=========>---------------------------------------------------------------------------------------------]   9% with 0 failures
 Completed [=========>---------------------------------------------------------------------------------------------]  10% with 0 failures
 Completed [==========>--------------------------------------------------------------------------------------------]  10% with 0 failures
 Completed [==========>--------------------------------------------------------------------------------------------]  11% with 0 failures
 Completed [===========>-------------------------------------------------------------------------------------------]  11% with 0 failures
 Completed [===========>-------------------------------------------------------------------------------------------]  12% with 0 failures
 Completed [============>------------------------------------------------------------------------------------------]  12% with 0 failures
 Completed [============>------------------------------------------------------------------------------------------]  13% with 0 failures
 Completed [=============>-----------------------------------------------------------------------------------------]  13% with 0 failures
 Completed [=============>-----------------------------------------------------------------------------------------]  14% with 0 failures
 Completed [==============>----------------------------------------------------------------------------------------]  14% with 0 failures
 Completed [==============>----------------------------------------------------------------------------------------]  15% with 0 failures
 Completed [===============>---------------------------------------------------------------------------------------]  15% with 0 failures
 Completed [===============>---------------------------------------------------------------------------------------]  16% with 0 failures
 Completed [================>--------------------------------------------------------------------------------------]  16% with 0 failures
 Completed [================>--------------------------------------------------------------------------------------]  17% with 0 failures
 Completed [=================>-------------------------------------------------------------------------------------]  17% with 0 failures
 Completed [=================>-------------------------------------------------------------------------------------]  18% with 0 failures
 Completed [==================>------------------------------------------------------------------------------------]  18% with 0 failures
 Completed [==================>------------------------------------------------------------------------------------]  19% with 0 failures
 Completed [===================>-----------------------------------------------------------------------------------]  19% with 0 failures
 Completed [===================>-----------------------------------------------------------------------------------]  20% with 0 failures
 Completed [====================>----------------------------------------------------------------------------------]  20% with 0 failures
 Completed [====================>----------------------------------------------------------------------------------]  21% with 0 failures
 Completed [=====================>---------------------------------------------------------------------------------]  21% with 0 failures
 Completed [=====================>---------------------------------------------------------------------------------]  22% with 0 failures
 Completed [======================>--------------------------------------------------------------------------------]  22% with 0 failures
 Completed [======================>--------------------------------------------------------------------------------]  23% with 0 failures
 Completed [=======================>-------------------------------------------------------------------------------]  23% with 0 failures
 Completed [=======================>-------------------------------------------------------------------------------]  24% with 0 failures
 Completed [========================>------------------------------------------------------------------------------]  24% with 0 failures
 Completed [========================>------------------------------------------------------------------------------]  25% with 0 failures
 Completed [=========================>-----------------------------------------------------------------------------]  25% with 0 failures
 Completed [=========================>-----------------------------------------------------------------------------]  26% with 0 failures
 Completed [==========================>----------------------------------------------------------------------------]  26% with 0 failures
 Completed [==========================>----------------------------------------------------------------------------]  27% with 0 failures
 Completed [===========================>---------------------------------------------------------------------------]  27% with 0 failures
 Completed [===========================>---------------------------------------------------------------------------]  28% with 0 failures
 Completed [============================>--------------------------------------------------------------------------]  28% with 0 failures
 Completed [============================>--------------------------------------------------------------------------]  29% with 0 failures
 Completed [=============================>-------------------------------------------------------------------------]  29% with 0 failures
 Completed [=============================>-------------------------------------------------------------------------]  30% with 0 failures
 Completed [==============================>------------------------------------------------------------------------]  30% with 0 failures
 Completed [==============================>------------------------------------------------------------------------]  31% with 0 failures
 Completed [===============================>-----------------------------------------------------------------------]  31% with 0 failures
 Completed [===============================>-----------------------------------------------------------------------]  32% with 0 failures
 Completed [================================>----------------------------------------------------------------------]  32% with 0 failures
 Completed [=================================>---------------------------------------------------------------------]  33% with 0 failures
 Completed [==================================>--------------------------------------------------------------------]  34% with 0 failures
 Completed [===================================>-------------------------------------------------------------------]  34% with 0 failures
 Completed [===================================>-------------------------------------------------------------------]  35% with 0 failures
 Completed [====================================>------------------------------------------------------------------]  35% with 0 failures
 Completed [====================================>------------------------------------------------------------------]  36% with 0 failures
 Completed [=====================================>-----------------------------------------------------------------]  36% with 0 failures
 Completed [=====================================>-----------------------------------------------------------------]  37% with 0 failures
 Completed [======================================>----------------------------------------------------------------]  37% with 0 failures
 Completed [======================================>----------------------------------------------------------------]  38% with 0 failures
 Completed [=======================================>---------------------------------------------------------------]  38% with 0 failures
 Completed [=======================================>---------------------------------------------------------------]  39% with 0 failures
 Completed [========================================>--------------------------------------------------------------]  39% with 0 failures
 Completed [========================================>--------------------------------------------------------------]  40% with 0 failures
 Completed [=========================================>-------------------------------------------------------------]  40% with 0 failures
 Completed [=========================================>-------------------------------------------------------------]  41% with 0 failures
 Completed [==========================================>------------------------------------------------------------]  41% with 0 failures
 Completed [==========================================>------------------------------------------------------------]  42% with 0 failures
 Completed [===========================================>-----------------------------------------------------------]  42% with 0 failures
 Completed [===========================================>-----------------------------------------------------------]  43% with 0 failures
 Completed [============================================>----------------------------------------------------------]  43% with 0 failures
 Completed [============================================>----------------------------------------------------------]  44% with 0 failures
 Completed [=============================================>---------------------------------------------------------]  44% with 0 failures
 Completed [=============================================>---------------------------------------------------------]  45% with 0 failures
 Completed [==============================================>--------------------------------------------------------]  45% with 0 failures
 Completed [==============================================>--------------------------------------------------------]  46% with 0 failures
 Completed [===============================================>-------------------------------------------------------]  46% with 0 failures
 Completed [===============================================>-------------------------------------------------------]  47% with 0 failures
 Completed [================================================>------------------------------------------------------]  47% with 0 failures
 Completed [================================================>------------------------------------------------------]  48% with 0 failures
 Completed [=================================================>-----------------------------------------------------]  48% with 0 failures
 Completed [=================================================>-----------------------------------------------------]  49% with 0 failures
 Completed [==================================================>----------------------------------------------------]  49% with 0 failures
 Completed [==================================================>----------------------------------------------------]  50% with 0 failures
 Completed [===================================================>---------------------------------------------------]  50% with 0 failures
 Completed [===================================================>---------------------------------------------------]  51% with 0 failures
 Completed [====================================================>--------------------------------------------------]  51% with 0 failures
 Completed [====================================================>--------------------------------------------------]  52% with 0 failures
 Completed [=====================================================>-------------------------------------------------]  52% with 0 failures
 Completed [=====================================================>-------------------------------------------------]  53% with 0 failures
 Completed [======================================================>------------------------------------------------]  53% with 0 failures
 Completed [======================================================>------------------------------------------------]  54% with 0 failures
 Completed [=======================================================>-----------------------------------------------]  54% with 0 failures
 Completed [=======================================================>-----------------------------------------------]  55% with 0 failures
 Completed [========================================================>----------------------------------------------]  55% with 0 failures
 Completed [========================================================>----------------------------------------------]  56% with 0 failures
 Completed [=========================================================>---------------------------------------------]  56% with 0 failures
 Completed [=========================================================>---------------------------------------------]  57% with 0 failures
 Completed [==========================================================>--------------------------------------------]  57% with 0 failures
 Completed [==========================================================>--------------------------------------------]  58% with 0 failures
 Completed [===========================================================>-------------------------------------------]  58% with 0 failures
 Completed [===========================================================>-------------------------------------------]  59% with 0 failures
 Completed [============================================================>------------------------------------------]  59% with 0 failures
 Completed [============================================================>------------------------------------------]  60% with 0 failures
 Completed [=============================================================>-----------------------------------------]  60% with 0 failures
 Completed [=============================================================>-----------------------------------------]  61% with 0 failures
 Completed [==============================================================>----------------------------------------]  61% with 0 failures
 Completed [==============================================================>----------------------------------------]  62% with 0 failures
 Completed [===============================================================>---------------------------------------]  62% with 0 failures
 Completed [===============================================================>---------------------------------------]  63% with 0 failures
 Completed [================================================================>--------------------------------------]  63% with 0 failures
 Completed [================================================================>--------------------------------------]  64% with 0 failures
 Completed [=================================================================>-------------------------------------]  64% with 0 failures
 Completed [=================================================================>-------------------------------------]  65% with 0 failures
 Completed [==================================================================>------------------------------------]  65% with 0 failures
 Completed [==================================================================>------------------------------------]  66% with 0 failures
 Completed [===================================================================>-----------------------------------]  66% with 0 failures
 Completed [====================================================================>----------------------------------]  67% with 0 failures
 Completed [=====================================================================>---------------------------------]  68% with 0 failures
 Completed [======================================================================>--------------------------------]  68% with 0 failures
 Completed [======================================================================>--------------------------------]  69% with 0 failures
 Completed [=======================================================================>-------------------------------]  69% with 0 failures
 Completed [=======================================================================>-------------------------------]  70% with 0 failures
 Completed [========================================================================>------------------------------]  70% with 0 failures
 Completed [========================================================================>------------------------------]  71% with 0 failures
 Completed [=========================================================================>-----------------------------]  71% with 0 failures
 Completed [=========================================================================>-----------------------------]  72% with 0 failures
 Completed [==========================================================================>----------------------------]  72% with 0 failures
 Completed [==========================================================================>----------------------------]  73% with 0 failures
 Completed [===========================================================================>---------------------------]  73% with 0 failures
 Completed [===========================================================================>---------------------------]  74% with 0 failures
 Completed [============================================================================>--------------------------]  74% with 0 failures
 Completed [============================================================================>--------------------------]  75% with 0 failures
 Completed [=============================================================================>-------------------------]  75% with 0 failures
 Completed [=============================================================================>-------------------------]  76% with 0 failures
 Completed [==============================================================================>------------------------]  76% with 0 failures
 Completed [==============================================================================>------------------------]  77% with 0 failures
 Completed [===============================================================================>-----------------------]  77% with 0 failures
 Completed [===============================================================================>-----------------------]  78% with 0 failures
 Completed [================================================================================>----------------------]  78% with 0 failures
 Completed [================================================================================>----------------------]  79% with 0 failures
 Completed [=================================================================================>---------------------]  79% with 0 failures
 Completed [=================================================================================>---------------------]  80% with 0 failures
 Completed [==================================================================================>--------------------]  80% with 0 failures
 Completed [==================================================================================>--------------------]  81% with 0 failures
 Completed [===================================================================================>-------------------]  81% with 0 failures
 Completed [===================================================================================>-------------------]  82% with 0 failures
 Completed [====================================================================================>------------------]  82% with 0 failures
 Completed [====================================================================================>------------------]  83% with 0 failures
 Completed [=====================================================================================>-----------------]  83% with 0 failures
 Completed [=====================================================================================>-----------------]  84% with 0 failures
 Completed [======================================================================================>----------------]  84% with 0 failures
 Completed [======================================================================================>----------------]  85% with 0 failures
 Completed [=======================================================================================>---------------]  85% with 0 failures
 Completed [=======================================================================================>---------------]  86% with 0 failures
 Completed [========================================================================================>--------------]  86% with 0 failures
 Completed [========================================================================================>--------------]  87% with 0 failures
 Completed [=========================================================================================>-------------]  87% with 0 failures
 Completed [=========================================================================================>-------------]  88% with 0 failures
 Completed [==========================================================================================>------------]  88% with 0 failures
 Completed [==========================================================================================>------------]  89% with 0 failures
 Completed [===========================================================================================>-----------]  89% with 0 failures
 Completed [===========================================================================================>-----------]  90% with 0 failures
 Completed [============================================================================================>----------]  90% with 0 failures
 Completed [============================================================================================>----------]  91% with 0 failures
 Completed [=============================================================================================>---------]  91% with 0 failures
 Completed [=============================================================================================>---------]  92% with 0 failures
 Completed [==============================================================================================>--------]  92% with 0 failures
 Completed [==============================================================================================>--------]  93% with 0 failures
 Completed [===============================================================================================>-------]  93% with 0 failures
 Completed [===============================================================================================>-------]  94% with 0 failures
 Completed [================================================================================================>------]  94% with 0 failures
 Completed [================================================================================================>------]  95% with 0 failures
 Completed [=================================================================================================>-----]  95% with 0 failures
 Completed [=================================================================================================>-----]  96% with 0 failures
 Completed [==================================================================================================>----]  96% with 0 failures
 Completed [==================================================================================================>----]  97% with 0 failures
 Completed [===================================================================================================>---]  97% with 0 failures
 Completed [===================================================================================================>---]  98% with 0 failures
 Completed [====================================================================================================>--]  98% with 0 failures
 Completed [====================================================================================================>--]  99% with 0 failures
 Completed [=====================================================================================================>-]  99% with 0 failures
 Completed [======================================================================================================>] 100% with 0 failures
 Completed [=======================================================================================================] 100% with 0 failures
                                                                                                                                         

Done!
Combining coefficients and standard errors
Calculating log-fold changes
Calculating likelihood ratio tests
Refitting on reduced model...

 Completed [====>--------------------------------------------------------------------------------------------------]   5% with 0 failures
 Completed [=====>-------------------------------------------------------------------------------------------------]   5% with 0 failures
 Completed [=====>-------------------------------------------------------------------------------------------------]   6% with 0 failures
 Completed [======>------------------------------------------------------------------------------------------------]   6% with 0 failures
 Completed [======>------------------------------------------------------------------------------------------------]   7% with 0 failures
 Completed [=======>-----------------------------------------------------------------------------------------------]   7% with 0 failures
 Completed [=======>-----------------------------------------------------------------------------------------------]   8% with 0 failures
 Completed [========>----------------------------------------------------------------------------------------------]   8% with 0 failures
 Completed [========>----------------------------------------------------------------------------------------------]   9% with 0 failures
 Completed [=========>---------------------------------------------------------------------------------------------]   9% with 0 failures
 Completed [=========>---------------------------------------------------------------------------------------------]  10% with 0 failures
 Completed [==========>--------------------------------------------------------------------------------------------]  10% with 0 failures
 Completed [==========>--------------------------------------------------------------------------------------------]  11% with 0 failures
 Completed [===========>-------------------------------------------------------------------------------------------]  11% with 0 failures
 Completed [===========>-------------------------------------------------------------------------------------------]  12% with 0 failures
 Completed [============>------------------------------------------------------------------------------------------]  12% with 0 failures
 Completed [============>------------------------------------------------------------------------------------------]  13% with 0 failures
 Completed [=============>-----------------------------------------------------------------------------------------]  13% with 0 failures
 Completed [=============>-----------------------------------------------------------------------------------------]  14% with 0 failures
 Completed [==============>----------------------------------------------------------------------------------------]  14% with 0 failures
 Completed [==============>----------------------------------------------------------------------------------------]  15% with 0 failures
 Completed [===============>---------------------------------------------------------------------------------------]  15% with 0 failures
 Completed [===============>---------------------------------------------------------------------------------------]  16% with 0 failures
 Completed [================>--------------------------------------------------------------------------------------]  16% with 0 failures
 Completed [================>--------------------------------------------------------------------------------------]  17% with 0 failures
 Completed [=================>-------------------------------------------------------------------------------------]  17% with 0 failures
 Completed [=================>-------------------------------------------------------------------------------------]  18% with 0 failures
 Completed [==================>------------------------------------------------------------------------------------]  18% with 0 failures
 Completed [==================>------------------------------------------------------------------------------------]  19% with 0 failures
 Completed [===================>-----------------------------------------------------------------------------------]  19% with 0 failures
 Completed [===================>-----------------------------------------------------------------------------------]  20% with 0 failures
 Completed [====================>----------------------------------------------------------------------------------]  20% with 0 failures
 Completed [====================>----------------------------------------------------------------------------------]  21% with 0 failures
 Completed [=====================>---------------------------------------------------------------------------------]  21% with 0 failures
 Completed [=====================>---------------------------------------------------------------------------------]  22% with 0 failures
 Completed [======================>--------------------------------------------------------------------------------]  22% with 0 failures
 Completed [======================>--------------------------------------------------------------------------------]  23% with 0 failures
 Completed [=======================>-------------------------------------------------------------------------------]  23% with 0 failures
 Completed [=======================>-------------------------------------------------------------------------------]  24% with 0 failures
 Completed [========================>------------------------------------------------------------------------------]  24% with 0 failures
 Completed [========================>------------------------------------------------------------------------------]  25% with 0 failures
 Completed [=========================>-----------------------------------------------------------------------------]  25% with 0 failures
 Completed [=========================>-----------------------------------------------------------------------------]  26% with 0 failures
 Completed [==========================>----------------------------------------------------------------------------]  26% with 0 failures
 Completed [==========================>----------------------------------------------------------------------------]  27% with 0 failures
 Completed [===========================>---------------------------------------------------------------------------]  27% with 0 failures
 Completed [===========================>---------------------------------------------------------------------------]  28% with 0 failures
 Completed [============================>--------------------------------------------------------------------------]  28% with 0 failures
 Completed [============================>--------------------------------------------------------------------------]  29% with 0 failures
 Completed [=============================>-------------------------------------------------------------------------]  29% with 0 failures
 Completed [=============================>-------------------------------------------------------------------------]  30% with 0 failures
 Completed [==============================>------------------------------------------------------------------------]  30% with 0 failures
 Completed [==============================>------------------------------------------------------------------------]  31% with 0 failures
 Completed [===============================>-----------------------------------------------------------------------]  31% with 0 failures
 Completed [===============================>-----------------------------------------------------------------------]  32% with 0 failures
 Completed [================================>----------------------------------------------------------------------]  32% with 0 failures
 Completed [=================================>---------------------------------------------------------------------]  33% with 0 failures
 Completed [==================================>--------------------------------------------------------------------]  34% with 0 failures
 Completed [===================================>-------------------------------------------------------------------]  34% with 0 failures
 Completed [===================================>-------------------------------------------------------------------]  35% with 0 failures
 Completed [====================================>------------------------------------------------------------------]  35% with 0 failures
 Completed [====================================>------------------------------------------------------------------]  36% with 0 failures
 Completed [=====================================>-----------------------------------------------------------------]  36% with 0 failures
 Completed [=====================================>-----------------------------------------------------------------]  37% with 0 failures
 Completed [======================================>----------------------------------------------------------------]  37% with 0 failures
 Completed [======================================>----------------------------------------------------------------]  38% with 0 failures
 Completed [=======================================>---------------------------------------------------------------]  38% with 0 failures
 Completed [=======================================>---------------------------------------------------------------]  39% with 0 failures
 Completed [========================================>--------------------------------------------------------------]  39% with 0 failures
 Completed [========================================>--------------------------------------------------------------]  40% with 0 failures
 Completed [=========================================>-------------------------------------------------------------]  40% with 0 failures
 Completed [=========================================>-------------------------------------------------------------]  41% with 0 failures
 Completed [==========================================>------------------------------------------------------------]  41% with 0 failures
 Completed [==========================================>------------------------------------------------------------]  42% with 0 failures
 Completed [===========================================>-----------------------------------------------------------]  42% with 0 failures
 Completed [===========================================>-----------------------------------------------------------]  43% with 0 failures
 Completed [============================================>----------------------------------------------------------]  43% with 0 failures
 Completed [============================================>----------------------------------------------------------]  44% with 0 failures
 Completed [=============================================>---------------------------------------------------------]  44% with 0 failures
 Completed [=============================================>---------------------------------------------------------]  45% with 0 failures
 Completed [==============================================>--------------------------------------------------------]  45% with 0 failures
 Completed [==============================================>--------------------------------------------------------]  46% with 0 failures
 Completed [===============================================>-------------------------------------------------------]  46% with 0 failures
 Completed [===============================================>-------------------------------------------------------]  47% with 0 failures
 Completed [================================================>------------------------------------------------------]  47% with 0 failures
 Completed [================================================>------------------------------------------------------]  48% with 0 failures
 Completed [=================================================>-----------------------------------------------------]  48% with 0 failures
 Completed [=================================================>-----------------------------------------------------]  49% with 0 failures
 Completed [==================================================>----------------------------------------------------]  49% with 0 failures
 Completed [==================================================>----------------------------------------------------]  50% with 0 failures
 Completed [===================================================>---------------------------------------------------]  50% with 0 failures
 Completed [===================================================>---------------------------------------------------]  51% with 0 failures
 Completed [====================================================>--------------------------------------------------]  51% with 0 failures
 Completed [====================================================>--------------------------------------------------]  52% with 0 failures
 Completed [=====================================================>-------------------------------------------------]  52% with 0 failures
 Completed [=====================================================>-------------------------------------------------]  53% with 0 failures
 Completed [======================================================>------------------------------------------------]  53% with 0 failures
 Completed [======================================================>------------------------------------------------]  54% with 0 failures
 Completed [=======================================================>-----------------------------------------------]  54% with 0 failures
 Completed [=======================================================>-----------------------------------------------]  55% with 0 failures
 Completed [========================================================>----------------------------------------------]  55% with 0 failures
 Completed [========================================================>----------------------------------------------]  56% with 0 failures
 Completed [=========================================================>---------------------------------------------]  56% with 0 failures
 Completed [=========================================================>---------------------------------------------]  57% with 0 failures
 Completed [==========================================================>--------------------------------------------]  57% with 0 failures
 Completed [==========================================================>--------------------------------------------]  58% with 0 failures
 Completed [===========================================================>-------------------------------------------]  58% with 0 failures
 Completed [===========================================================>-------------------------------------------]  59% with 0 failures
 Completed [============================================================>------------------------------------------]  59% with 0 failures
 Completed [============================================================>------------------------------------------]  60% with 0 failures
 Completed [=============================================================>-----------------------------------------]  60% with 0 failures
 Completed [=============================================================>-----------------------------------------]  61% with 0 failures
 Completed [==============================================================>----------------------------------------]  61% with 0 failures
 Completed [==============================================================>----------------------------------------]  62% with 0 failures
 Completed [===============================================================>---------------------------------------]  62% with 0 failures
 Completed [===============================================================>---------------------------------------]  63% with 0 failures
 Completed [================================================================>--------------------------------------]  63% with 0 failures
 Completed [================================================================>--------------------------------------]  64% with 0 failures
 Completed [=================================================================>-------------------------------------]  64% with 0 failures
 Completed [=================================================================>-------------------------------------]  65% with 0 failures
 Completed [==================================================================>------------------------------------]  65% with 0 failures
 Completed [==================================================================>------------------------------------]  66% with 0 failures
 Completed [===================================================================>-----------------------------------]  66% with 0 failures
 Completed [====================================================================>----------------------------------]  67% with 0 failures
 Completed [=====================================================================>---------------------------------]  68% with 0 failures
 Completed [======================================================================>--------------------------------]  68% with 0 failures
 Completed [======================================================================>--------------------------------]  69% with 0 failures
 Completed [=======================================================================>-------------------------------]  69% with 0 failures
 Completed [=======================================================================>-------------------------------]  70% with 0 failures
 Completed [========================================================================>------------------------------]  70% with 0 failures
 Completed [========================================================================>------------------------------]  71% with 0 failures
 Completed [=========================================================================>-----------------------------]  71% with 0 failures
 Completed [=========================================================================>-----------------------------]  72% with 0 failures
 Completed [==========================================================================>----------------------------]  72% with 0 failures
 Completed [==========================================================================>----------------------------]  73% with 0 failures
 Completed [===========================================================================>---------------------------]  73% with 0 failures
 Completed [===========================================================================>---------------------------]  74% with 0 failures
 Completed [============================================================================>--------------------------]  74% with 0 failures
 Completed [============================================================================>--------------------------]  75% with 0 failures
 Completed [=============================================================================>-------------------------]  75% with 0 failures
 Completed [=============================================================================>-------------------------]  76% with 0 failures
 Completed [==============================================================================>------------------------]  76% with 0 failures
 Completed [==============================================================================>------------------------]  77% with 0 failures
 Completed [===============================================================================>-----------------------]  77% with 0 failures
 Completed [===============================================================================>-----------------------]  78% with 0 failures
 Completed [================================================================================>----------------------]  78% with 0 failures
 Completed [================================================================================>----------------------]  79% with 0 failures
 Completed [=================================================================================>---------------------]  79% with 0 failures
 Completed [=================================================================================>---------------------]  80% with 0 failures
 Completed [==================================================================================>--------------------]  80% with 0 failures
 Completed [==================================================================================>--------------------]  81% with 0 failures
 Completed [===================================================================================>-------------------]  81% with 0 failures
 Completed [===================================================================================>-------------------]  82% with 0 failures
 Completed [====================================================================================>------------------]  82% with 0 failures
 Completed [====================================================================================>------------------]  83% with 0 failures
 Completed [=====================================================================================>-----------------]  83% with 0 failures
 Completed [=====================================================================================>-----------------]  84% with 0 failures
 Completed [======================================================================================>----------------]  84% with 0 failures
 Completed [======================================================================================>----------------]  85% with 0 failures
 Completed [=======================================================================================>---------------]  85% with 0 failures
 Completed [=======================================================================================>---------------]  86% with 0 failures
 Completed [========================================================================================>--------------]  86% with 0 failures
 Completed [========================================================================================>--------------]  87% with 0 failures
 Completed [=========================================================================================>-------------]  87% with 0 failures
 Completed [=========================================================================================>-------------]  88% with 0 failures
 Completed [==========================================================================================>------------]  88% with 0 failures
 Completed [==========================================================================================>------------]  89% with 0 failures
 Completed [===========================================================================================>-----------]  89% with 0 failures
 Completed [===========================================================================================>-----------]  90% with 0 failures
 Completed [============================================================================================>----------]  90% with 0 failures
 Completed [============================================================================================>----------]  91% with 0 failures
 Completed [=============================================================================================>---------]  91% with 0 failures
 Completed [=============================================================================================>---------]  92% with 0 failures
 Completed [==============================================================================================>--------]  92% with 0 failures
 Completed [==============================================================================================>--------]  93% with 0 failures
 Completed [===============================================================================================>-------]  93% with 0 failures
 Completed [===============================================================================================>-------]  94% with 0 failures
 Completed [================================================================================================>------]  94% with 0 failures
 Completed [================================================================================================>------]  95% with 0 failures
 Completed [=================================================================================================>-----]  95% with 0 failures
 Completed [=================================================================================================>-----]  96% with 0 failures
 Completed [==================================================================================================>----]  96% with 0 failures
 Completed [==================================================================================================>----]  97% with 0 failures
 Completed [===================================================================================================>---]  97% with 0 failures
 Completed [===================================================================================================>---]  98% with 0 failures
 Completed [====================================================================================================>--]  98% with 0 failures
 Completed [====================================================================================================>--]  99% with 0 failures
 Completed [=====================================================================================================>-]  99% with 0 failures
 Completed [======================================================================================================>] 100% with 0 failures
 Completed [=======================================================================================================] 100% with 0 failures
                                                                                                                                         

Done!
cca_top_markers = cca_markers %>%
    group_by(cluster) %>%
    slice_min(n = 5, order_by = p_val_adj)
VlnPlot(cca_seurat, features = c("Dab2", "Kcnab1"))

VlnPlot(cca_seurat, features = c("Cenpf", "Pttg1"))

VlnPlot(cca_seurat, features = c("Upk1b", "Timp3"))

NA
NA

dab2 involved in endothelial stuf -> 0 is probably induced cardiomyocyet Upk1b is involved in epithelial stuff -> 2 is porbably fibroblasts 1 - induced fibroblasts

Idents(cca_seurat)  = "RNA_snn_res.1"
cca_seurat = RenameIdents(cca_seurat, `0` = "iCM")
cca_seurat = RenameIdents(cca_seurat, `1` = "iFib")
cca_seurat = RenameIdents(cca_seurat, `2` = "Fib")
DimPlot(cca_seurat, label = TRUE)

SC Transform

seurat.sc = CreateSeuratObject(counts = exp)
seurat.sc = SCTransform(seurat.sc)
seurat.sc = RunPCA(seurat.sc, features =  VariableFeatures(seurat.sc))
identified_cells = identified_cells[match(rownames(seurat.sc@meta.data), rownames(identified_cells)),]
seurat.sc@meta.data$cc_paper = identified_cells$CC
seurat.sc@meta.data$cat_paper = identified_cells$stage

seurat.sc = RunUMAP(seurat.sc, dims = 1:15)
seurat.sc = FindNeighbors(seurat.sc, dims = 1:15)
seurat.sc = FindClusters(seurat.sc, resolution = 1.75)
seurat.sc = CellCycleScoring(seurat.sc, s.features = s.genes, g2m.features = g2m.genes)
clusters = DimPlot(seurat.sc, group.by = "SCT_snn_res.1.75", label = TRUE, reduction = "umap")
real_condition = DimPlot(seurat.sc, group.by = "cc_paper", label = TRUE, reduction = "umap") 
phase = DimPlot(seurat.sc, group.by = "Phase", label = TRUE, reduction = "umap") 
cat = DimPlot(seurat.sc, group.by = "cat_paper", label = TRUE, reduction = "umap") 

clusters|real_condition|phase|cat
---
title: "R Notebook"
output: html_notebook
---

This is an [R Markdown](http://rmarkdown.rstudio.com) Notebook. When you execute code within the notebook, the results appear beneath the code. 

Try executing this chunk by clicking the *Run* button within the chunk or by placing your cursor inside it and pressing *Cmd+Shift+Enter*. 

```{r}
library("devtools")
install_github("jw156605/SLICER")
library(Seurat)
library(readr)
library(tidyverse)
library(HGC) 
library(latticeExtra)
library(lattice) 
library(RColorBrewer)
library(clusterProfiler)
library(org.Mm.eg.db)
library(AnnotationDbi)
```


```{r}
exp = read_csv("normalized_data.csv")
exp = discard(exp,~all(is.na(.) |.  == ""))
exp = distinct(exp, `...1`, .keep_all = TRUE)
# filtering out the reprogramming transcription factors 
exp = filter(exp, !`...1`%in% c("Mef2c", "Gata4", "Tbx5"))
exp = column_to_rownames(exp, var="...1")

```
```{r}

seurat.obj = CreateSeuratObject(counts = exp)
```
```{r}
seurat.obj = NormalizeData(seurat.obj)
seurat.obj = FindVariableFeatures(seurat.obj, selection.method =  "vst", nfeatures = 10000)
all.genes = rownames(seurat.obj)
seurat.obj = ScaleData(seurat.obj, features = all.genes)
seurat.obj = RunPCA(seurat.obj, features =  VariableFeatures(seurat.obj))

```
```{r}
ElbowPlot(seurat.obj)
```

```{r}
seurat.obj = FindNeighbors(seurat.obj, dims = 1:15)
```

```{r}
seurat.obj = FindClusters(seurat.obj, resolution = 1.75)
```
```{r}
identified_cells = read.csv("paper_cell_states.csv", row.names = 1, header=TRUE)
```
```{r}
identified_cells = identified_cells[match(rownames(seurat.obj@meta.data), rownames(identified_cells)),]
seurat.obj@meta.data$cc_paper = identified_cells$CC
seurat.obj@meta.data$cat_paper = identified_cells$stage
seurat.obj@meta.data$cc_hclust = "CCI"
seurat.obj@meta.data[active_cells,]$cc_hclust = "CCA"

```


```{r}
Idents(seurat.obj)  = "RNA_snn_res.1.75"
```

```{r}
seurat.obj = RunUMAP(seurat.obj, dims = 1:15)
```
```{r}
seurat.obj = RunTSNE(seurat.obj, dims = 1:15)
DimPlot(seurat.obj, reduction = "tsne", group.by = 'RNA_snn_res.1.75')
``` 

```{r}
markers = FindAllMarkers(seurat.obj, logfc.threshold =  0.25, min.pct = 0.1, only.pos = FALSE, test.use = 'MAST')
```
```{r}
top_markers = markers %>%
    group_by(cluster) %>%
    slice_max(n = 2, order_by = avg_log2FC)
```

```{r}
FeaturePlot(seurat.obj, features = c("Dhrs3"), min.cutoff = 'q10')
```
```{r}
VlnPlot(seurat.obj, features = c("Rbp1", "Dhrs3"))
VlnPlot(seurat.obj, features = c("Fstl1", "Bgn"))
VlnPlot(seurat.obj, features = c("Serpinh1", "Dsp"))
VlnPlot(seurat.obj, features = c("Prc1", "Birc5"))
```
```{r}
## cell cycle 
s.genes <- str_to_title(cc.genes$s.genes)
g2m.genes <- str_to_title(cc.genes$g2m.genes)

seurat.obj = CellCycleScoring(seurat.obj, s.features = s.genes, g2m.features = g2m.genes)
```


```{r}
clusters = DimPlot(seurat.obj, group.by = "RNA_snn_res.1.75", label = TRUE, reduction = "umap")
real_condition = DimPlot(seurat.obj, group.by = "cc_paper", label = TRUE, reduction = "umap") 
phase = DimPlot(seurat.obj, group.by = "Phase", label = TRUE, reduction = "umap") 
cat = DimPlot(seurat.obj, group.by = "cc_hclust", label = TRUE, reduction = "umap") 

clusters|real_condition|phase|cat


```

## subsetting the cells that fit with hclust and performing clustering on each group 

```{r}
cca_seurat = subset(x = seurat.obj, subset = cc_hclust == "CCA")
cci_seurat = subset(x = seurat.obj, subset = cc_hclust == "CCI")

```

## clustering CCI cels 

```{r}
cci_seurat = FindNeighbors(cci_seurat, dims = 1:15)
cci_seurat = FindClusters(cci_seurat, resolution = 1)
```

```{r}
cl= DimPlot(cci_seurat, group.by = "RNA_snn_res.1",label = TRUE)
pap = DimPlot(cci_seurat, group.by = "cat_paper", label = TRUE)
cl|pap
```
## identifying CCI cells 

```{r}
cci_markers = FindAllMarkers(cci_seurat, logfc.threshold =  0.25, min.pct = 0.1, only.pos = FALSE, test.use = 'MAST')
```
```{r}
cci_top_markers = cci_markers %>%
    group_by(cluster) %>%
    slice_min(n = 5, order_by = p_val_adj)
```

```{r}
VlnPlot(cci_seurat, features = c("Fstl1", "Bgn"))
VlnPlot(cci_seurat, features = c("Tnni3", "Smpx"))
VlnPlot(cci_seurat, features = c("Serpinh1", "Dsp"))
VlnPlot(cci_seurat, features = c("Clca2", "Rbp1"))
VlnPlot(cci_seurat, features = c("Cfh", "B4galt1"))

```
#### 

Fstl1 involved in endothelial cell differentiation and endothelial cell migration and Bgn is a gene that is used for connective tissue metabolism -> lower expression -> cluster 0 = iCM 

Tnni3, smpx, dsp used for cardiomycoytes -> cluster 2 = pre-iCM, cluster 1 and 3 are still fibroblasts 

cluseter 1 further away from cluster 0 = fibroblastr
clusetr 3 = induced fibroblasts

```{r}
Idents(cci_seurat)  = "RNA_snn_res.1"
cci_seurat = RenameIdents(cci_seurat, `0` = "iCM")
cci_seurat = RenameIdents(cci_seurat, `1` = "Fib")
cci_seurat = RenameIdents(cci_seurat, `2` = "piCM")
cci_seurat = RenameIdents(cci_seurat, `3` = "iFib")

```

```{r}
DimPlot(cci_seurat, label = TRUE)

```
## clustering CCA cells


```{r}
cca_seurat = FindNeighbors(cca_seurat, dims = 1:15)
cca_seurat = FindClusters(cca_seurat, resolution = 1)
```

```{r}
cl= DimPlot(cca_seurat, group.by = "RNA_snn_res.1",label = TRUE)
pap = DimPlot(cca_seurat, group.by = "cat_paper", label = TRUE)
cl|pap
```
## identifying CCA cells 

```{r}
cca_markers = FindAllMarkers(cca_seurat, logfc.threshold =  0.25, min.pct = 0.1, only.pos = FALSE, test.use = 'MAST')
```
```{r}
cca_top_markers = cca_markers %>%
    group_by(cluster) %>%
    slice_min(n = 5, order_by = p_val_adj)
```

```{r}
VlnPlot(cca_seurat, features = c("Dab2", "Kcnab1"))
VlnPlot(cca_seurat, features = c("Cenpf", "Pttg1"))
VlnPlot(cca_seurat, features = c("Upk1b", "Timp3"))


```
#### 

dab2 involved in endothelial stuf -> 0 is probably induced cardiomyocyet
Upk1b is involved in epithelial stuff -> 2 is porbably fibroblasts 
1 - induced fibroblasts

```{r}
Idents(cca_seurat)  = "RNA_snn_res.1"
cca_seurat = RenameIdents(cca_seurat, `0` = "iCM")
cca_seurat = RenameIdents(cca_seurat, `1` = "iFib")
cca_seurat = RenameIdents(cca_seurat, `2` = "Fib")


```

```{r}
DimPlot(cca_seurat, label = TRUE)

```

## SC Transform       
```{r}
seurat.sc = CreateSeuratObject(counts = exp)
seurat.sc = SCTransform(seurat.sc)
```
```{r}
seurat.sc = RunPCA(seurat.sc, features =  VariableFeatures(seurat.sc))
```

```{r}
identified_cells = identified_cells[match(rownames(seurat.sc@meta.data), rownames(identified_cells)),]
seurat.sc@meta.data$cc_paper = identified_cells$CC
seurat.sc@meta.data$cat_paper = identified_cells$stage

seurat.sc = RunUMAP(seurat.sc, dims = 1:15)
seurat.sc = FindNeighbors(seurat.sc, dims = 1:15)
seurat.sc = FindClusters(seurat.sc, resolution = 1.75)
```

```{r}
seurat.sc = CellCycleScoring(seurat.sc, s.features = s.genes, g2m.features = g2m.genes)
```

```{r}
clusters = DimPlot(seurat.sc, group.by = "SCT_snn_res.1.75", label = TRUE, reduction = "umap")
real_condition = DimPlot(seurat.sc, group.by = "cc_paper", label = TRUE, reduction = "umap") 
phase = DimPlot(seurat.sc, group.by = "Phase", label = TRUE, reduction = "umap") 
cat = DimPlot(seurat.sc, group.by = "cat_paper", label = TRUE, reduction = "umap") 

clusters|real_condition|phase|cat

```

